From hpm at bioinfo-user.org.uk  Wed Mar  2 04:25:05 2011
From: hpm at bioinfo-user.org.uk (Hamish McWilliam)
Date: Wed, 2 Mar 2011 09:25:05 +0000
Subject: [EMBOSS] accessing emboss ftp site
In-Reply-To: <AANLkTimGr7Y8ZKSRbqX87NN2_PHjF1BMWeyEVLAGQ=es@mail.gmail.com>
References: <6F57C2D1-8927-420C-940C-C6EC0C62AABE@gmail.com>
	<4BD0DB9B.5050005@sonsorol.org>
	<l2o5cba6b9f1004230756gf04316acq8519b375ce29e0d8@mail.gmail.com>
	<4BD1C05D.5010109@sonsorol.org>
	<FBBE6420-C5DA-4070-A67C-E7AC5A97F920@gmail.com>
	<AANLkTinK7fYE5U5uBmXiUaKh-BL61JI48WoRiRjlO9kD@mail.gmail.com>
	<4C50193D.5060500@bioteam.net>
	<AANLkTinGKTWZtj8EHBw1jmYnEO3X4Z2rQHSAM5OpE9KH@mail.gmail.com>
	<4C516A84.1050706@bioteam.net>
	<AANLkTimGr7Y8ZKSRbqX87NN2_PHjF1BMWeyEVLAGQ=es@mail.gmail.com>
Message-ID: <AANLkTinS_sS_6UMeVj2-hJRJE9XvzUvmmhHKzc+nooMR@mail.gmail.com>

Hi Chris,

You had any luck figuring out what is causing this issue with the FTP site?

Hamish

On 29 July 2010 14:46, Hamish McWilliam <hpm at bioinfo-user.org.uk> wrote:
> Hi Chris,
>
>> I did have to turn on support in VSFTPd for "ls -R" because it was
>> considered a possible resource drain or DOS target on large directories but
>> you are right that the extended mode passive stuff does not work. It does
>> not seem to be a firewall issue on the server and I don't think our upstream
>> Juniper SSG intrusion device is interfering.
>
> FWIW I get the same behavior when using passive or "active" FTP modes.
>
>> Can I ask what you are ?trying to accomplish? A mirror process? Can we get
>> around this problem via an anonymous RSYNC service pointing at the anonymous
>> FTP root? Passwordless SSH access for a mirror script that uses "rsync -avz
>> -e ssh ..." or similar?
>
> I'm trying to update the EMBL-EBI mirror of the EMBOSS software
> (ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/), this uses Mirror
> (ftp://ftp.ebi.ac.uk/pub/software/unix/mirror.tar.Z) to do the
> updates. As you can tell from the files in the directory this mirror
> no longer works, since it cannot get the listing of files. In fact it
> fails silently so I can't tell when the problem started.
>
>> vsftpd fits our needs for secure anonymous FTP server, if there is an easier
>> route to getting your needs sorted I might want to look at that rather than
>> going down deep into vsftp internals or swapping out the server software.
>
> From a few experiments with our vsftpd setup (CentOS 5.x, vsftpd
> 2.0.5) this looks to be supported by default, other than the -R thing.
>
> From a little Google it could be some interaction with the other
> components (http://www.ncftp.com/ncftpd/doc/misc/ftp_and_firewalls.html)
> where they don't recognize the FTP command correctly and choose the
> wrong mode, but it seems unlikely. Does it work if you run directly
> against the box?
>
> Hamish
>
>> Hamish McWilliam wrote:
>>>
>>> Hi Chris,
>>>
>>>> I can't seem to replicate this at all with any of my available FTP
>>>> clients
>>>> or browser-based FTP clients. It works for me from both Mac OS X clients
>>>> as
>>>> well as a CentOS 5.4 based Linux system.
>>>>
>>>> Is there an FTP client / OS combo that seems in particular not to work?
>>>
>>> This affects all clients I've tried.
>>>
>>> ?From your transcript, you are not running the commands required to see
>>> the issue:
>>>
>>> - 'ls' or 'dir' without options works
>>> - 'ls' or 'dir' with options hangs and eventually gives a timeout. FTP
>>> mirror systems often use -lRat as options to 'ls' to get all the files
>>> for a particular branch.
>>>
>>> $ ftp emboss.open-bio.org
>>> Connected to emboss.open-bio.org.
>>> 220 (vsFTPd 2.0.1)
>>> 530 Please login with USER and PASS.
>>> 530 Please login with USER and PASS.
>>> KERBEROS_V4 rejected as an authentication type
>>> Name (emboss.open-bio.org:hpm): ftp
>>> 331 Please specify the password.
>>> Password:
>>> 230 Login successful.
>>> Remote system type is UNIX.
>>> Using binary mode to transfer files.
>>> ftp> ?cd /pub/EMBOSS/fixes
>>> 250 Directory successfully changed.
>>> ftp> ?ls
>>> 227 Entering Passive Mode (208,94,50,58,51,71)
>>> 150 Here comes the directory listing.
>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ? ? 385 Jul 21 09:25 README.fixes
>>> -rwxrwxr-x ? ?1 501 ? ? ?503 ? ? ? ?506140 Jul 21 09:25 configure
>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ? ?5405 Jul 21 09:25 mysql.m4
>>> drwxrwsr-x ? ?4 501 ? ? ?503 ? ? ? ? ?4096 Jul 21 09:26 patches
>>> 226 Directory send OK.
>>> ftp> ?ls -lRat
>>> 227 Entering Passive Mode (208,94,50,58,31,88)
>>> *HANG*
>>>
>>> Compare with the equivalent session against the EMBL-EBI FTP site:
>>>
>>> $ ftp ftp.ebi.ac.uk
>>> Connected to ftp.ebi.ac.uk.
>>> 220-
>>> 220- ftp1.ebi.ac.uk FTP server
>>> 220-
>>> 220- WARNING: please note that the private part of this ftp service
>>> 220- has been migrated to ftp-private.ebi.ac.uk on 3rd June 2010.
>>> 220
>>> 530 Please login with USER and PASS.
>>> 530 Please login with USER and PASS.
>>> KERBEROS_V4 rejected as an authentication type
>>> Name (ftp.ebi.ac.uk:hpm): ftp
>>> 331 Please specify the password.
>>> Password:
>>> 230 Login successful.
>>> Remote system type is UNIX.
>>> Using binary mode to transfer files.
>>> ftp> ?cd /pub/software/unix/EMBOSS/fixes
>>> 250 Directory successfully changed.
>>> ftp> ?ls
>>> 227 Entering Passive Mode (193,62,193,4,238,107)
>>> 150 Here comes the directory listing.
>>> -r--r--r-- ? ?1 ftp ? ? ?ftp ? ? ? ? ? 180 Jan 15 ?2010 README.fixes
>>> 226 Directory send OK.
>>> ftp> ?ls -lRat
>>> 227 Entering Passive Mode (193,62,193,4,36,65)
>>> 150 Here comes the directory listing.
>>> .:
>>> drwxr-xr-x ? ?3 ftp ? ? ?ftp ? ? ? ? ?4096 Jan 18 ?2010 ..
>>> drwxr-xr-x ? ?2 ftp ? ? ?ftp ? ? ? ? ?4096 Jan 18 ?2010 .
>>> -r--r--r-- ? ?1 ftp ? ? ?ftp ? ? ? ? ? 180 Jan 15 ?2010 README.fixes
>>> 226 Directory send OK.
>>> ftp> ?bye
>>> 221 Goodbye.
>>>
>>> All the best,
>>>
>>> Hamish
>>>
>>>> Here is one example:
>>>>
>>>>> dag-static:~ dag$ ftp emboss.open-bio.org
>>>>> Connected to emboss.open-bio.org.
>>>>> 220 (vsFTPd 2.0.1)
>>>>> Name (emboss.open-bio.org:dag): anonymous
>>>>> 331 Please specify the password.
>>>>> Password:
>>>>> 230 Login successful.
>>>>> Remote system type is UNIX.
>>>>> Using binary mode to transfer files.
>>>>> ftp> ?dir
>>>>> 229 Entering Extended Passive Mode (|||54472|)
>>>>> 150 Here comes the directory listing.
>>>>> drwxr-xr-x ? ?8 14 ? ? ? 50 ? ? ? ? ? 4096 May 22 ?2006 pub
>>>>> 226 Directory send OK.
>>>>> ftp> ?cd pub/EMBOSS
>>>>> 250 Directory successfully changed.
>>>>> ftp> ?ls
>>>>> 229 Entering Extended Passive Mode (|||38343|)
>>>>> 150 Here comes the directory listing.
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?389856 Jul 21 09:25
>>>>> CBSTOOLS-1.0.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?426218 Jul 21 09:25
>>>>> DOMAINATRIX-0.1.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?441025 Jul 21 09:25
>>>>> DOMALIGN-0.1.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?452787 Jul 21 09:25
>>>>> DOMSEARCH-0.1.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ?23572243 Jul 19 13:41
>>>>> EMBOSS-6.3.1.tar.gz
>>>>> lrwxrwxrwx ? ?1 501 ? ? ?503 ? ? ? ? ? ?19 Jul 19 13:42
>>>>> EMBOSS-latest.tar.gz -> ?EMBOSS-6.3.1.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?373798 Jul 21 09:25 EMNU-1.05.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?415096 Jul 21 09:25
>>>>> ESIM4-1.0.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?569581 Jul 21 09:25
>>>>> HMMER-2.3.2.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?350791 Jul 21 09:25
>>>>> IPRSCAN-4.3.1.tar.gz
>>>>> drwxrwsr-x ? ?7 501 ? ? ?503 ? ? ? ? ?4096 Feb 01 ?2006 Jemboss
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?513418 Jul 21 09:25
>>>>> MEMENEW-4.0.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?823636 Jul 21 09:25
>>>>> MIRA-2.8.2.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?435315 Jul 21 09:25 MSE-3.0.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?328540 Jul 21 09:25
>>>>> MYEMBOSS-6.3.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?359488 Jul 21 09:25
>>>>> MYEMBOSSDEMO-6.3.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? 1667760 Jul 21 09:25
>>>>> PHYLIPNEW-3.69.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?571008 Jul 21 09:25
>>>>> SIGNATURE-0.1.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?531604 Jul 21 09:25
>>>>> STRUCTURE-0.1.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?386287 Jul 21 09:25
>>>>> TOPO-2.0.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?652433 Jul 21 09:25
>>>>> VIENNA-1.7.2.tar.gz
>>>>> drwxrwsr-x ? ?3 522 ? ? ?503 ? ? ? ? ?4096 Aug 21 ?2006 contrib
>>>>> drwxrwsr-x ? ?2 501 ? ? ?503 ? ? ? ? ?4096 Nov 11 ?2005 doc
>>>>> drwxrwsr-x ? ?3 501 ? ? ?503 ? ? ? ? ?4096 Jul 21 09:25 fixes
>>>>> drwxrwsr-x ? 14 501 ? ? ?503 ? ? ? ? ?4096 Jul 19 13:39 old
>>>>> drwxrwsr-x ? ?2 501 ? ? ?503 ? ? ? ? ?4096 Jul 06 ?2005 tutorials
>>>>> drwxrwsr-x ? ?4 501 ? ? ?503 ? ? ? ? ?4096 Jul 19 13:36 windows
>>>>> 226 Directory send OK.
>>>>> ftp>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Hamish McWilliam wrote:
>>>>>
>>>>> Hi Chris,
>>>>>
>>>>> I'm also seeing problems with the FTP site, but using Mirror rather
>>>>> than Transmit, it looks like the server does not like options being
>>>>> specified to the LIST command:
>>>>>
>>>>> Scanning remote directory /pub/EMBOSS
>>>>> ---> ? ?CWD /pub/EMBOSS
>>>>> 250 Directory successfully changed.
>>>>> ---> ? ?TYPE A
>>>>> 200 Switching to ASCII mode.
>>>>> ---> ? ?PORT 172,21,22,1,171,245
>>>>> 200 PORT command successful. Consider using PASV.
>>>>> ---> ? ?PASV
>>>>> 227 Entering Passive Mode (208,94,50,58,104,178)
>>>>> ---> ? ?LIST -lat
>>>>> timed out
>>>>> Cannot get remote directory listing because: timed out
>>>>> Cannot get remote directory details (/pub/EMBOSS)
>>>>> disconnecting from emboss.open-bio.org
>>>>>
>>>>> Trying it with a command line client I get the response to hang if I
>>>>> try using any options to ls or dir, without options they are fine.
>>>>>
>>>>> All the best,
>>>>>
>>>>> Hamish
>>>>>
>>>>> On 29 May 2010 03:44, Koen van der Drift<koenvanderdrift at gmail.com>
>>>>> ?wrote:
>>>>>>
>>>>>> Hi Chris,
>>>>>>
>>>>>> Did you have a chance to look at this? Just tried again, and Transmit
>>>>>> still
>>>>>> won't let me access the emboss ftp site.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> - Koen.
>>>>>>
>>>>>>
>>>>>> On Apr 23, 2010, at 11:44 AM, Chris Dagdigian wrote:
>>>>>>
>>>>>>> In the last few months the open-bio.org servers switched datacenters,
>>>>>>> IP
>>>>>>> addresses and firewall/IDS appliances. Lots of juicy things to look at
>>>>>>> and
>>>>>>> debug.
>>>>>>>
>>>>>>> Koen - if you have a chance can you send me the IP address that you
>>>>>>> are
>>>>>>> using to connect from? I might be able to find some relevant log
>>>>>>> entries
>>>>>>> with that info.
>>>>>>>
>>>>>>> -Chris
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Koen van der Drift wrote:
>>>>>>>>
>>>>>>>> Just for the record, it used to work with Transmit, this is only from
>>>>>>>> the last few months.
>>>>>>>>
>>>>>>>> - Koen.
>>>>>>>>
>>>>>>>> On Thu, Apr 22, 2010 at 7:28 PM, Chris Dagdigian<dag at sonsorol.org>
>>>>>>>> ?wrote:
>>>>>>>>>
>>>>>>>>> Might be an issue with the Juniper Netscreen firewall/IDS security
>>>>>>>>> appliance
>>>>>>>>> that sits upstream of the EMBOSS FTP server. I'll take a look at the
>>>>>>>>> security logs and alerts.
>>>>>>>>>
>>>>>>>>> -Chris
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Koen van der Drift wrote:
>>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> For a while now I am unable to access the emboss ftp site using the
>>>>>>>>>> OS
>>>>>>>>>> X
>>>>>>>>>> client Transmit. Loggin in works fine, but it chokes on the LIST
>>>>>>>>>> command. I have no problems accessing it from the command line. I
>>>>>>>>>> have
>>>>>>>>>> added the output from Transmit below. I don't know if this is a
>>>>>>>>>> Transmit
>>>>>>>>>> or emboss issue, but just wanted to let you know.
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> - Koen.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Transmit 3.6.9 Session Transcript
>>>>>>>>>> LibNcFTP 3.2.1 (August 13, 2007) compiled for UNIX
>>>>>>>>>> Uname: Darwin|exile.local|9.8.0|Darwin Kernel Version 9.8.0: Wed
>>>>>>>>>> Jul
>>>>>>>>>> 15
>>>>>>>>>> 16:57:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_PPC|Power Macintosh
>>>>>>>>>> 220: (vsFTPd 2.0.1)
>>>>>>>>>> Connected to emboss.open-bio.org.
>>>>>>>>>> Cmd: USER anonymous
>>>>>>>>>> 331: Please specify the password.
>>>>>>>>>> Cmd: PASS NcFTP@
>>>>>>>>>> 230: Login successful.
>>>>>>>>>> Cmd: TYPE A
>>>>>>>>>> 200: Switching to ASCII mode.
>>>>>>>>>> Logged in to emboss.open-bio.org as anonymous.
>>>>>>>>>> Cmd: SYST
>>>>>>>>>> 215: UNIX Type: L8
>>>>>>>>>> Cmd: PWD
>>>>>>>>>> 257: "/"
>>>>>>>>>> Cmd: CWD /pub/EMBOSS/fixes
>>>>>>>>>> 250: Directory successfully changed.
>>>>>>>>>> Cmd: PWD
>>>>>>>>>> 257: "/pub/EMBOSS/fixes"
>>>>>>>>>> Cmd: PASV
>>>>>>>>>> 227: Entering Passive Mode (208,94,50,58,83,232)
>>>>>>>>>> Cmd: LIST -a
>>>>>>>>>> Could not read reply from control connection -- timed out.
>>>>>>>>>> (SReadline
>>>>>>>>>> 1)
>>>>>>>>>> 220: (vsFTPd 2.0.1)
>>>>>>>>>> Connected to emboss.open-bio.org.
>>>>>>>>>> Cmd: USER anonymous
>>>>>>>>>> 331: Please specify the password.
>>>>>>>>>> Cmd: PASS NcFTP@
>>>>>>>>>> 230: Login successful.
>>>>>>>>>> Logged in to emboss.open-bio.org as anonymous.
>>>>>>>>>> Cmd: SYST
>>>>>>>>>> 215: UNIX Type: L8
>>>>>>>>>> Cmd: PWD
>>>>>>>>>> 257: "/"
>>>>>>>>>> Cmd: CWD /pub/EMBOSS/fixes
>>>>>>>>>> 250: Directory successfully changed.
>>>>>>>>>> Cmd: PWD
>>>>>>>>>> 257: "/pub/EMBOSS/fixes"
>>>>>>>>>> Cmd: PASV
>>>>>>>>>> 227: Entering Passive Mode (208,94,50,58,222,100)
>>>>>>>>>> Cmd: LIST -a
>>>>>>>>>> Could not read reply from control connection -- timed out.
>>>>>>>>>> (SReadline
>>>>>>>>>> 1)
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> EMBOSS mailing list
>>>>>>>>>> EMBOSS at lists.open-bio.org
>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>>>>
>>>>>> _______________________________________________
>>>>>> EMBOSS mailing list
>>>>>> EMBOSS at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>>>>
>>>>>
>>>>>
>>>
>>>
>>>
>>
>
>
>
> --
> ----
> "Saying the internet has changed dramatically over the last five years
> is clich? ? the internet is always changing dramatically" - Craig
> Labovitz, Arbor Networks.
>



-- 
----
"Saying the internet has changed dramatically over the last five years
is clich? ? the internet is always changing dramatically" - Craig
Labovitz, Arbor Networks.


From wolfgang.rumpf at rescentris.com  Wed Mar  9 15:00:41 2011
From: wolfgang.rumpf at rescentris.com (Wolfgang Rumpf)
Date: Wed, 9 Mar 2011 15:00:41 -0500
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
	ajSeqdbInit
Message-ID: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>

I have an Emboss installation I'm using for teaching purposes.  It was
working just fine until a few days ago, when I updated my OS to Ubuntu 10.10
(from 10.4).  Now I'm getting this error, specifically when I run fdnapars.
I'm worried that more might be broken, and I can't find anything useful via
google when I search for the error.  Can anyone shed some light on what's
going on here?

fdnapars: symbol lookup error: /usr/lib/libnucleus.so.6: undefined
symbol: ajSeqdbInit



Cheers,

Wolfgang

----------------------
Wolfgang Rumpf, Ph.D.
Product Specialist, Rescentris Inc
Adjunct Faculty, UMUC Dept. of Biotechnology
----------------------

From egorleg at gmail.com  Wed Mar  9 18:10:13 2011
From: egorleg at gmail.com (Kevin Egan)
Date: Wed, 9 Mar 2011 23:10:13 +0000
Subject: [EMBOSS] HELP! DOTMATCHER
Message-ID: <AANLkTin38ZwuTepHrf8MU8RsBhOXBOfvWDHLoFOQwq6B@mail.gmail.com>

Hi

I entered the information as follows

dotmatcher -asequence cam3.txt -bsequence TCH3A.txt [-matrixfile EDNAFULL]
[-windowsize 10] [-threshold 70]

but got a 'too many parameters' error message.

Does anyone know how to enter my own values for window length etc?

Regards,

Kevin

From idrummon at receptor.mgh.harvard.edu  Wed Mar  9 18:31:24 2011
From: idrummon at receptor.mgh.harvard.edu (Iain Drummond)
Date: Wed, 09 Mar 2011 18:31:24 -0500
Subject: [EMBOSS] HELP! DOTMATCHER
In-Reply-To: <AANLkTin38ZwuTepHrf8MU8RsBhOXBOfvWDHLoFOQwq6B@mail.gmail.com>
Message-ID: <C99D77FC.1F2B%idrummon@receptor.mgh.harvard.edu>

Hi Kevin,

For starters i would get rid of the square brackets ("[]") in your command;
i don't think these are necessary.

Iain Drummond


On 3/9/11 6:10 PM, "Kevin Egan" <egorleg at gmail.com> wrote:

> Hi
> 
> I entered the information as follows
> 
> dotmatcher -asequence cam3.txt -bsequence TCH3A.txt [-matrixfile EDNAFULL]
> [-windowsize 10] [-threshold 70]
> 
> but got a 'too many parameters' error message.
> 
> Does anyone know how to enter my own values for window length etc?
> 
> Regards,
> 
> Kevin
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
> 




The information in this e-mail is intended only for the person to whom it is
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From marvin.stodolsky at gmail.com  Wed Mar  9 19:48:41 2011
From: marvin.stodolsky at gmail.com (Marvin Stodolsky)
Date: Wed, 9 Mar 2011 19:48:41 -0500
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
	ajSeqdbInit
In-Reply-To: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>
Message-ID: <AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>

Wolfgang

RE:  undefined symbol: ajSeqdbInit
While not an expert at all, on Emboss code,
this type of error is typically due to (Emboss) binaries Not Yet
being compiled with the newer linux-header resources.  Pending that
compilation by the Emboss maintenance team, if you run the compile
from Emboss source code on your own  Ubuntu 10.10 system, all will
likely be  OK.

Check if linux-headers are installed on your System with:
$ sudo apt-get update
$ sudo apt-get install linux-headers-$(uname -r)

You could also just reinstall and boot under the last kernel supporting Emboss.
Typically linux is backward compatible to prior kernels, for a
considerable period.
Just search out the prior linux-image package at: http://packages.ubuntu.com

MarvS
scanModem maintainer



On Wed, Mar 9, 2011 at 3:00 PM, Wolfgang Rumpf
<wolfgang.rumpf at rescentris.com> wrote:
> I have an Emboss installation I'm using for teaching purposes. ?It was
> working just fine until a few days ago, when I updated my OS to Ubuntu 10.10
> (from 10.4). ?Now I'm getting this error, specifically when I run fdnapars.
> I'm worried that more might be broken, and I can't find anything useful via
> google when I search for the error. ?Can anyone shed some light on what's
> going on here?
>
> fdnapars: symbol lookup error: /usr/lib/libnucleus.so.6: undefined
> symbol: ajSeqdbInit
>
>
>
> Cheers,
>
> Wolfgang
>
> ----------------------
> Wolfgang Rumpf, Ph.D.
> Product Specialist, Rescentris Inc
> Adjunct Faculty, UMUC Dept. of Biotechnology
> ----------------------
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>


From pmr at ebi.ac.uk  Wed Mar  9 20:00:56 2011
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 10 Mar 2011 01:00:56 +0000
Subject: [EMBOSS] HELP! DOTMATCHER
In-Reply-To: <C99D77FC.1F2B%idrummon@receptor.mgh.harvard.edu>
References: <C99D77FC.1F2B%idrummon@receptor.mgh.harvard.edu>
Message-ID: <4D7822C8.6040309@ebi.ac.uk>

On 09/03/2011 23:31, Iain Drummond wrote:
> Hi Kevin,
>
> For starters i would get rid of the square brackets ("[]") in your command;
> i don't think these are necessary.

That's the right answer. Qualifiers on the command line must start with 
'-' otherwise they are counted as 'parameters'. The square brackets are 
hiding the crucial dashes.

regards,

Peter Rice
EMBOSS Team

> On 3/9/11 6:10 PM, "Kevin Egan"<egorleg at gmail.com>  wrote:
>
>> Hi
>>
>> I entered the information as follows
>>
>> dotmatcher -asequence cam3.txt -bsequence TCH3A.txt [-matrixfile EDNAFULL]
>> [-windowsize 10] [-threshold 70]
>>
>> but got a 'too many parameters' error message.

From charles-listes-emboss at plessy.org  Wed Mar  9 20:37:00 2011
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Thu, 10 Mar 2011 10:37:00 +0900
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
 ajSeqdbInit
In-Reply-To: <AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>
	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>
Message-ID: <20110310013700.GC11010@merveille.plessy.net>

Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a ?crit :
> 
> RE:  undefined symbol: ajSeqdbInit
> While not an expert at all, on Emboss code,
> this type of error is typically due to (Emboss) binaries Not Yet
> being compiled with the newer linux-header resources.  Pending that
> compilation by the Emboss maintenance team, if you run the compile
> from Emboss source code on your own  Ubuntu 10.10 system, all will
> likely be  OK.

Dear Wolfgang,

you can also give a try to the emboss and embassy-phylip from 11.04 Ubuntu
distribution. If you can install them on 10.10, they should work well, and
they are up to date.

http://packages.ubuntu.com/natty/emboss
http://packages.ubuntu.com/natty/embassy-phylip

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

From wolfgang.rumpf at rescentris.com  Thu Mar 10 10:26:38 2011
From: wolfgang.rumpf at rescentris.com (Wolfgang Rumpf)
Date: Thu, 10 Mar 2011 10:26:38 -0500
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
	ajSeqdbInit
In-Reply-To: <20110310013700.GC11010@merveille.plessy.net>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>
	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>
	<20110310013700.GC11010@merveille.plessy.net>
Message-ID: <BD9C610C-7ADE-4D73-9094-94CE5DFD1F50@mac.com>

So as I understand it my options are:

1.  Boot with an older kernel - probably the latest one from 10.4, if it works with 10.10;
2.  Recompile EMBOSS myself;
3.  Download and install the 11.04 (unreleased) Emboss/Embassy installs;
4.  Wait for 11.04 to come out 

Of all of these the "simplest" (other than just waiting) would probably be to try to boot with an older kernel - I don't want to bring the rest of the EMBOSS system down for an extended time period, perhaps very extended if the compilation/install doesn't go as planned.

Sound about right?

Wolfgang

Dr. Wolfgang Rumpf
Product Specialist, Rescentris Inc.
--------------------------------------------------------
wolfgang.rumpf at rescentris.com

Mobile - (614) 638-6797
Skype - wolfgang.rumpf




On Mar 9, 2011, at 8:37 PM, Charles Plessy wrote:

> Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a ?crit :
>> 
>> RE:  undefined symbol: ajSeqdbInit
>> While not an expert at all, on Emboss code,
>> this type of error is typically due to (Emboss) binaries Not Yet
>> being compiled with the newer linux-header resources.  Pending that
>> compilation by the Emboss maintenance team, if you run the compile
>> from Emboss source code on your own  Ubuntu 10.10 system, all will
>> likely be  OK.
> 
> Dear Wolfgang,
> 
> you can also give a try to the emboss and embassy-phylip from 11.04 Ubuntu
> distribution. If you can install them on 10.10, they should work well, and
> they are up to date.
> 
> http://packages.ubuntu.com/natty/emboss
> http://packages.ubuntu.com/natty/embassy-phylip
> 
> Have a nice day,
> 
> -- 
> Charles Plessy
> Debian Med packaging team
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss



From marvin.stodolsky at gmail.com  Thu Mar 10 12:58:37 2011
From: marvin.stodolsky at gmail.com (Marvin Stodolsky)
Date: Thu, 10 Mar 2011 12:58:37 -0500
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
	ajSeqdbInit
In-Reply-To: <BD9C610C-7ADE-4D73-9094-94CE5DFD1F50@mac.com>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>
	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>
	<20110310013700.GC11010@merveille.plessy.net>
	<BD9C610C-7ADE-4D73-9094-94CE5DFD1F50@mac.com>
Message-ID: <AANLkTimOW9i0hbmo2RPuhOCE8RnGNZ08dVH7=QxP5NNU@mail.gmail.com>

Wolfgang

> 1.  Boot with an older kernel - probably the latest one from 10.4, if it works with 10.10;
really is expected to be trouble free.  Linux strives to maintain
backward compatibility.

In the course of aiding modem users, I have and boot with numerous
older kernels on my Systems.
Your worst case scenario is that a bootup with an older kernel will
fail.  Then you will have to reboot with the current one. Merely
having an older kernel installed will IN NO WAY interfere with usage
of more recent kernels.

Marvin

On Thu, Mar 10, 2011 at 10:26 AM, Wolfgang Rumpf
<wolfgang.rumpf at rescentris.com> wrote:
> So as I understand it my options are:
>
> 1. ?Boot with an older kernel - probably the latest one from 10.4, if it works with 10.10;
> 2. ?Recompile EMBOSS myself;
> 3. ?Download and install the 11.04 (unreleased) Emboss/Embassy installs;
> 4. ?Wait for 11.04 to come out
>
> Of all of these the "simplest" (other than just waiting) would probably be to try to boot with an older kernel - I don't want to bring the rest of the EMBOSS system down for an extended time period, perhaps very extended if the compilation/install doesn't go as planned.
>
> Sound about right?
>
> Wolfgang
>
> Dr. Wolfgang Rumpf
> Product Specialist, Rescentris Inc.
> --------------------------------------------------------
> wolfgang.rumpf at rescentris.com
>
> Mobile - (614) 638-6797
> Skype - wolfgang.rumpf
>
>
>
>
> On Mar 9, 2011, at 8:37 PM, Charles Plessy wrote:
>
>> Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a ?crit :
>>>
>>> RE: ?undefined symbol: ajSeqdbInit
>>> While not an expert at all, on Emboss code,
>>> this type of error is typically due to (Emboss) binaries Not Yet
>>> being compiled with the newer linux-header resources. ?Pending that
>>> compilation by the Emboss maintenance team, if you run the compile
>>> from Emboss source code on your own ?Ubuntu 10.10 system, all will
>>> likely be ?OK.
>>
>> Dear Wolfgang,
>>
>> you can also give a try to the emboss and embassy-phylip from 11.04 Ubuntu
>> distribution. If you can install them on 10.10, they should work well, and
>> they are up to date.
>>
>> http://packages.ubuntu.com/natty/emboss
>> http://packages.ubuntu.com/natty/embassy-phylip
>>
>> Have a nice day,
>>
>> --
>> Charles Plessy
>> Debian Med packaging team
>> http://www.debian.org/devel/debian-med
>> Tsurumi, Kanagawa, Japan
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>


From henrikki.almusa at helsinki.fi  Thu Mar 10 13:27:42 2011
From: henrikki.almusa at helsinki.fi (Henrikki Almusa)
Date: Thu, 10 Mar 2011 20:27:42 +0200
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error
	-	ajSeqdbInit
In-Reply-To: <BD9C610C-7ADE-4D73-9094-94CE5DFD1F50@mac.com>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>	<20110310013700.GC11010@merveille.plessy.net>
	<BD9C610C-7ADE-4D73-9094-94CE5DFD1F50@mac.com>
Message-ID: <4D79181E.1050007@helsinki.fi>

On 2011-03-10 17:26, Wolfgang Rumpf wrote:
> So as I understand it my options are:
>
> 1.  Boot with an older kernel - probably the latest one from 10.4, if it works with 10.10;
> 2.  Recompile EMBOSS myself;
> 3.  Download and install the 11.04 (unreleased) Emboss/Embassy installs;
> 4.  Wait for 11.04 to come out
>
> Of all of these the "simplest" (other than just waiting) would probably be to try to boot with an older kernel - I don't want to bring the rest of the EMBOSS system down for an extended time period, perhaps very extended if the compilation/install doesn't go as planned.
>
> Sound about right?

The error message complains about missing library file libnucleus.so.6 
which was probably removed in update as there was no dependency on it 
(within the package lists). So here's a way to fix it:
  - go to packages.ubuntu.com and search for a package with file called 
libnucleus.so.6
  - get result which tells you that it is in package libnucleus6
  - install that named package with your favourite tool (for example 
apt-get)


> Wolfgang
>
> Dr. Wolfgang Rumpf
> Product Specialist, Rescentris Inc.
> --------------------------------------------------------
> wolfgang.rumpf at rescentris.com
>
> Mobile - (614) 638-6797
> Skype - wolfgang.rumpf
>
>
>
>
> On Mar 9, 2011, at 8:37 PM, Charles Plessy wrote:
>
>> Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a ?crit :
>>>
>>> RE:  undefined symbol: ajSeqdbInit
>>> While not an expert at all, on Emboss code,
>>> this type of error is typically due to (Emboss) binaries Not Yet
>>> being compiled with the newer linux-header resources.  Pending that
>>> compilation by the Emboss maintenance team, if you run the compile
>>> from Emboss source code on your own  Ubuntu 10.10 system, all will
>>> likely be  OK.
>>
>> Dear Wolfgang,
>>
>> you can also give a try to the emboss and embassy-phylip from 11.04 Ubuntu
>> distribution. If you can install them on 10.10, they should work well, and
>> they are up to date.
>>
>> http://packages.ubuntu.com/natty/emboss
>> http://packages.ubuntu.com/natty/embassy-phylip
>>
>> Have a nice day,
>>
>> --
>> Charles Plessy
>> Debian Med packaging team
>> http://www.debian.org/devel/debian-med
>> Tsurumi, Kanagawa, Japan
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>


-- 
Henrikki Almusa


From marvin.stodolsky at gmail.com  Thu Mar 10 18:48:46 2011
From: marvin.stodolsky at gmail.com (Marvin Stodolsky)
Date: Thu, 10 Mar 2011 18:48:46 -0500
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
	ajSeqdbInit
In-Reply-To: <4D79181E.1050007@helsinki.fi>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>
	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>
	<20110310013700.GC11010@merveille.plessy.net>
	<BD9C610C-7ADE-4D73-9094-94CE5DFD1F50@mac.com>
	<4D79181E.1050007@helsinki.fi>
Message-ID: <AANLkTikYZuk8mypJ5_MteeO0tCE2wtGbphM2wVpGrXK+@mail.gmail.com>

There is a:
http://packages.ubuntu.com/maverick/libnucleus6

$ sudo apt-get update
$ sudo apt-get libnucleus6

should do all necessary.

MarvS

On Thu, Mar 10, 2011 at 1:27 PM, Henrikki Almusa
<henrikki.almusa at helsinki.fi> wrote:
> On 2011-03-10 17:26, Wolfgang Rumpf wrote:
>>
>> So as I understand it my options are:
>>
>> 1. ?Boot with an older kernel - probably the latest one from 10.4, if it
>> works with 10.10;
>> 2. ?Recompile EMBOSS myself;
>> 3. ?Download and install the 11.04 (unreleased) Emboss/Embassy installs;
>> 4. ?Wait for 11.04 to come out
>>
>> Of all of these the "simplest" (other than just waiting) would probably be
>> to try to boot with an older kernel - I don't want to bring the rest of the
>> EMBOSS system down for an extended time period, perhaps very extended if the
>> compilation/install doesn't go as planned.
>>
>> Sound about right?
>
> The error message complains about missing library file libnucleus.so.6 which
> was probably removed in update as there was no dependency on it (within the
> package lists). So here's a way to fix it:
> ?- go to packages.ubuntu.com and search for a package with file called
> libnucleus.so.6
> ?- get result which tells you that it is in package libnucleus6
> ?- install that named package with your favourite tool (for example apt-get)
>
>
>> Wolfgang
>>
>> Dr. Wolfgang Rumpf
>> Product Specialist, Rescentris Inc.
>> --------------------------------------------------------
>> wolfgang.rumpf at rescentris.com
>>
>> Mobile - (614) 638-6797
>> Skype - wolfgang.rumpf
>>
>>
>>
>>
>> On Mar 9, 2011, at 8:37 PM, Charles Plessy wrote:
>>
>>> Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a ?crit :
>>>>
>>>> RE: ?undefined symbol: ajSeqdbInit
>>>> While not an expert at all, on Emboss code,
>>>> this type of error is typically due to (Emboss) binaries Not Yet
>>>> being compiled with the newer linux-header resources. ?Pending that
>>>> compilation by the Emboss maintenance team, if you run the compile
>>>> from Emboss source code on your own ?Ubuntu 10.10 system, all will
>>>> likely be ?OK.
>>>
>>> Dear Wolfgang,
>>>
>>> you can also give a try to the emboss and embassy-phylip from 11.04
>>> Ubuntu
>>> distribution. If you can install them on 10.10, they should work well,
>>> and
>>> they are up to date.
>>>
>>> http://packages.ubuntu.com/natty/emboss
>>> http://packages.ubuntu.com/natty/embassy-phylip
>>>
>>> Have a nice day,
>>>
>>> --
>>> Charles Plessy
>>> Debian Med packaging team
>>> http://www.debian.org/devel/debian-med
>>> Tsurumi, Kanagawa, Japan
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>
>
> --
> Henrikki Almusa
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>


From wolfgang.rumpf at gmail.com  Thu Mar 10 21:24:07 2011
From: wolfgang.rumpf at gmail.com (Wolfgang Rumpf)
Date: Thu, 10 Mar 2011 21:24:07 -0500
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
	ajSeqdbInit
In-Reply-To: <AANLkTikYZuk8mypJ5_MteeO0tCE2wtGbphM2wVpGrXK+@mail.gmail.com>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>	<20110310013700.GC11010@merveille.plessy.net>	<BD9C610C-7ADE-4D73-9094-94CE5DFD1F50@mac.com>	<4D79181E.1050007@helsinki.fi>
	<AANLkTikYZuk8mypJ5_MteeO0tCE2wtGbphM2wVpGrXK+@mail.gmail.com>
Message-ID: <4D7987C7.7020501@gmail.com>

Everything I have tried has failed.   I have uninstalled and reinstalled 
the entire EMBOSS/EMBASSY suite.  I have booted from the previous 
kernel.  Recompilation is a bit beyond me, I fear - what are the chances 
that this will just be fixed when 11.04 rolls out?  Has anyone else had 
this problem?

What's perplexing is that this has happened on both of my Ubuntu 
systems; there's nothing that was caused by me "tinkering" - this 
happened after the update to 10.10.  Why didn't this get caught - am I 
the only person using Phylip in Emboss Explorer?

On 03/10/2011 06:48 PM, Marvin Stodolsky wrote:
> There is a:
> http://packages.ubuntu.com/maverick/libnucleus6
>
> $ sudo apt-get update
> $ sudo apt-get libnucleus6
>
> should do all necessary.
>
> MarvS
>
> On Thu, Mar 10, 2011 at 1:27 PM, Henrikki Almusa
> <henrikki.almusa at helsinki.fi>  wrote:
>> On 2011-03-10 17:26, Wolfgang Rumpf wrote:
>>> So as I understand it my options are:
>>>
>>> 1.  Boot with an older kernel - probably the latest one from 10.4, if it
>>> works with 10.10;
>>> 2.  Recompile EMBOSS myself;
>>> 3.  Download and install the 11.04 (unreleased) Emboss/Embassy installs;
>>> 4.  Wait for 11.04 to come out
>>>
>>> Of all of these the "simplest" (other than just waiting) would probably be
>>> to try to boot with an older kernel - I don't want to bring the rest of the
>>> EMBOSS system down for an extended time period, perhaps very extended if the
>>> compilation/install doesn't go as planned.
>>>
>>> Sound about right?
>> The error message complains about missing library file libnucleus.so.6 which
>> was probably removed in update as there was no dependency on it (within the
>> package lists). So here's a way to fix it:
>>   - go to packages.ubuntu.com and search for a package with file called
>> libnucleus.so.6
>>   - get result which tells you that it is in package libnucleus6
>>   - install that named package with your favourite tool (for example apt-get)
>>
>>
>>> Wolfgang
>>>
>>> Dr. Wolfgang Rumpf
>>> Product Specialist, Rescentris Inc.
>>> --------------------------------------------------------
>>> wolfgang.rumpf at rescentris.com
>>>
>>> Mobile - (614) 638-6797
>>> Skype - wolfgang.rumpf
>>>
>>>
>>>
>>>
>>> On Mar 9, 2011, at 8:37 PM, Charles Plessy wrote:
>>>
>>>> Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a ?crit :
>>>>> RE:  undefined symbol: ajSeqdbInit
>>>>> While not an expert at all, on Emboss code,
>>>>> this type of error is typically due to (Emboss) binaries Not Yet
>>>>> being compiled with the newer linux-header resources.  Pending that
>>>>> compilation by the Emboss maintenance team, if you run the compile
>>>>> from Emboss source code on your own  Ubuntu 10.10 system, all will
>>>>> likely be  OK.
>>>> Dear Wolfgang,
>>>>
>>>> you can also give a try to the emboss and embassy-phylip from 11.04
>>>> Ubuntu
>>>> distribution. If you can install them on 10.10, they should work well,
>>>> and
>>>> they are up to date.
>>>>
>>>> http://packages.ubuntu.com/natty/emboss
>>>> http://packages.ubuntu.com/natty/embassy-phylip
>>>>
>>>> Have a nice day,
>>>>
>>>> --
>>>> Charles Plessy
>>>> Debian Med packaging team
>>>> http://www.debian.org/devel/debian-med
>>>> Tsurumi, Kanagawa, Japan
>>>> _______________________________________________
>>>> EMBOSS mailing list
>>>> EMBOSS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>
>>
>> --
>> Henrikki Almusa
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss


From wolfgang.rumpf at gmail.com  Thu Mar 10 21:26:44 2011
From: wolfgang.rumpf at gmail.com (Wolfgang Rumpf)
Date: Thu, 10 Mar 2011 21:26:44 -0500
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
	ajSeqdbInit
In-Reply-To: <20110310013700.GC11010@merveille.plessy.net>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>
	<20110310013700.GC11010@merveille.plessy.net>
Message-ID: <4D798864.9090801@gmail.com>

Also tried and failed - apparently there were dependencies that couldn't 
be resolved.

On 03/09/2011 08:37 PM, Charles Plessy wrote:
> Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a ?crit :
>> RE:  undefined symbol: ajSeqdbInit
>> While not an expert at all, on Emboss code,
>> this type of error is typically due to (Emboss) binaries Not Yet
>> being compiled with the newer linux-header resources.  Pending that
>> compilation by the Emboss maintenance team, if you run the compile
>> from Emboss source code on your own  Ubuntu 10.10 system, all will
>> likely be  OK.
> Dear Wolfgang,
>
> you can also give a try to the emboss and embassy-phylip from 11.04 Ubuntu
> distribution. If you can install them on 10.10, they should work well, and
> they are up to date.
>
> http://packages.ubuntu.com/natty/emboss
> http://packages.ubuntu.com/natty/embassy-phylip
>
> Have a nice day,
>


From charles-listes-emboss at plessy.org  Fri Mar 11 10:54:06 2011
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Sat, 12 Mar 2011 00:54:06 +0900
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
 ajSeqdbInit
In-Reply-To: <4D798864.9090801@gmail.com>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>
	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>
	<20110310013700.GC11010@merveille.plessy.net>
	<4D798864.9090801@gmail.com>
Message-ID: <20110311155406.GQ2316@merveille.plessy.net>

Le Thu, Mar 10, 2011 at 09:26:44PM -0500, Wolfgang Rumpf a ?crit :
> Also tried and failed - apparently there were dependencies that
> couldn't be resolved.

I have prepared unofficial backports of EMBOSS 6.3.1 and EMBASSY-PHYLIP 3.69

https://launchpad.net/~plessy/+archive/plessy/+sourcepub/1547062/+listing-archive-extra
https://launchpad.net/~plessy/+archive/plessy/+sourcepub/1547739/+listing-archive-extra

(the second one is scheduled to be built in 2 hours, so I can not guarantee that it
will be available)

Can you try them ?

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

From wolfgang.rumpf at gmail.com  Mon Mar 14 13:49:57 2011
From: wolfgang.rumpf at gmail.com (Wolfgang Rumpf)
Date: Mon, 14 Mar 2011 13:49:57 -0400
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
	ajSeqdbInit
In-Reply-To: <20110311155406.GQ2316@merveille.plessy.net>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>
	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>
	<20110310013700.GC11010@merveille.plessy.net>
	<4D798864.9090801@gmail.com>
	<20110311155406.GQ2316@merveille.plessy.net>
Message-ID: <E6E1C183-5C21-43C5-92EE-F459C8705CCE@gmail.com>

Now when I run the application I get this error in fdnapars:

"Error:  Unable to read sequence '/var/lib/emboss-explorer/output/672342/.sequence'
Died:  fdnapars terminated:  Bad value for ' -sequence' with -auto defined"

I looked in that directory and all that was in there was a .sequence file that looked just fine (it was my input file)....any ideas what went wrong?  Running fdnapars from the command line also results in an error reading the sequence file (it's one I use for testing, worked fine previously)....


Wolfgang

Dr. Wolfgang Rumpf
Product Specialist, Rescentris Inc.
Adjunct Faculty, Dept. of Biotechnology, UMUC
--------------------------------------------------------
wolfgang.rumpf at rescentris.com
wolfgang.rumpf at gmail.com

Mobile - (614) 638-6797
Skype - wolfgang.rumpf



On Mar 11, 2011, at 10:54 AM, Charles Plessy wrote:

> Le Thu, Mar 10, 2011 at 09:26:44PM -0500, Wolfgang Rumpf a ?crit :
>> Also tried and failed - apparently there were dependencies that
>> couldn't be resolved.
> 
> I have prepared unofficial backports of EMBOSS 6.3.1 and EMBASSY-PHYLIP 3.69
> 
> https://launchpad.net/~plessy/+archive/plessy/+sourcepub/1547062/+listing-archive-extra
> https://launchpad.net/~plessy/+archive/plessy/+sourcepub/1547739/+listing-archive-extra
> 
> (the second one is scheduled to be built in 2 hours, so I can not guarantee that it
> will be available)
> 
> Can you try them ?
> 
> Have a nice day,
> 
> -- 
> Charles Plessy
> Debian Med packaging team,
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan



From marvin.stodolsky at gmail.com  Tue Mar 15 13:27:00 2011
From: marvin.stodolsky at gmail.com (Marvin Stodolsky)
Date: Tue, 15 Mar 2011 13:27:00 -0400
Subject: [EMBOSS] trimming mRNA to coding region, enroute to dicodon analysis
Message-ID: <AANLkTik9xu64sNwm1NYNddD4JCdPEj1LU2z6ZnV9fHB7@mail.gmail.com>

Starting with a large mRNA  fasta repository,
what is the route to generating a derivative with the untranslated
leader and post-stop codon segments trimmed off the mRNAs

This is enroute to a dicodon usage analysis, already written as a BASH
script calling PERL modules.
If anyone is interested in such applications, let me know.
pdc (parse dicodons) works fine, taking about a second per pre-trimmed
mRNA as it retreives from a FASTA repository.
But before providing it to a Novice community, some fool proofing best be done.

Marvin.Stodolsky at gmail.com

From wolfgang.rumpf at gmail.com  Tue Mar 15 16:49:47 2011
From: wolfgang.rumpf at gmail.com (Wolfgang Rumpf)
Date: Tue, 15 Mar 2011 16:49:47 -0400
Subject: [EMBOSS] Vienna in Emboss/Emboss-Explorer on Ubuntu?
Message-ID: <FA6E6854-923D-4EF4-B554-4C8F60461E54@gmail.com>

One of the ideas I try to teach in my bioinformatics class is RNA folding - and as such I'd love to add an RNA folding algorithm to my bioinformatics server.  It seems like the "easiest" path might be Vienna since there's an EMBOSS port of it.  I'm not sure how to proceed, however - I've downloaded the source (VIENNA-1.7.2) and know the rough procedure for getting it installed, but I want it to "hook in" to my existing Ubuntu EMBOSS-Explorer (which is how my students access all of the other analyses we do).  Any ideas how to modify the installation to install to the correct path so that it will be available in my existing applications list?

Any help appreciated - thanks in advance!


Wolfgang

Dr. Wolfgang Rumpf
Product Specialist, Rescentris Inc.
Adjunct Faculty, Dept. of Biotechnology, UMUC
--------------------------------------------------------
wolfgang.rumpf at rescentris.com
wolfgang.rumpf at gmail.com

Mobile - (614) 638-6797
Skype - wolfgang.rumpf





From david.bauer at bayer.com  Wed Mar 16 04:13:25 2011
From: david.bauer at bayer.com (david.bauer at bayer.com)
Date: Wed, 16 Mar 2011 09:13:25 +0100
Subject: [EMBOSS] Antwort:  trimming mRNA to coding region,
 enroute to dicodon analysis
In-Reply-To: <AANLkTik9xu64sNwm1NYNddD4JCdPEj1LU2z6ZnV9fHB7@mail.gmail.com>
Message-ID: <OF3F3EDBF1.495F0438-ONC1257855.002C6B49-C1257855.002D2CB8@bayer.de>

Hi,

I already sometimes thought it would be nice to have an option for getorf 
which would return just the longest ORF it finds. 
Here is what I use to get the coding part from an mRNA sequence if there 
is no feature table information:

> getorf test.fa -find 1 -norev | infoseq -only -len -desc -filter | sort 
-nr | head -1 | tr -d "[]" | awk '{print "seqret test.fa -sb "$2" -send 
"$4}'

HTH,
David.

emboss-bounces at lists.open-bio.org schrieb am 15/03/2011 18:27:00:

> Starting with a large mRNA  fasta repository,
> what is the route to generating a derivative with the untranslated
> leader and post-stop codon segments trimmed off the mRNAs
> 
> This is enroute to a dicodon usage analysis, already written as a BASH
> script calling PERL modules.
> If anyone is interested in such applications, let me know.
> pdc (parse dicodons) works fine, taking about a second per pre-trimmed
> mRNA as it retreives from a FASTA repository.
> But before providing it to a Novice community, some fool proofing 
> best be done.
> 
> Marvin.Stodolsky at gmail.com
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss

From david.bauer at bayer.com  Wed Mar 16 05:25:28 2011
From: david.bauer at bayer.com (david.bauer at bayer.com)
Date: Wed, 16 Mar 2011 10:25:28 +0100
Subject: [EMBOSS] Antwort:  Vienna in Emboss/Emboss-Explorer on Ubuntu?
In-Reply-To: <FA6E6854-923D-4EF4-B554-4C8F60461E54@gmail.com>
Message-ID: <OF827F9BEE.E42D2CBA-ONC1257855.00331892-C1257855.0033C616@bayer.de>

Hi,

the emboss-explorer creates the html menu on the fly by calling the emboss 
program wossname.
So if you install the Vienna embassy package just in the same place like 
the main emboss, the vrnafold etc. should appear in the emboss-explorer.
But I'm not using it on Ubuntu so I do not know if there are any Ubuntu 
specific issues.

HTH,
David.

emboss-bounces at lists.open-bio.org schrieb am 15/03/2011 21:49:47:

> One of the ideas I try to teach in my bioinformatics class is RNA 
> folding - and as such I'd love to add an RNA folding algorithm to my
> bioinformatics server.  It seems like the "easiest" path might be 
> Vienna since there's an EMBOSS port of it.  I'm not sure how to 
> proceed, however - I've downloaded the source (VIENNA-1.7.2) and 
> know the rough procedure for getting it installed, but I want it to 
> "hook in" to my existing Ubuntu EMBOSS-Explorer (which is how my 
> students access all of the other analyses we do).  Any ideas how to 
> modify the installation to install to the correct path so that it 
> will be available in my existing applications list?
> 
> Any help appreciated - thanks in advance!
> 
> 
> Wolfgang
> 
> Dr. Wolfgang Rumpf
> Product Specialist, Rescentris Inc.
> Adjunct Faculty, Dept. of Biotechnology, UMUC
> --------------------------------------------------------
> wolfgang.rumpf at rescentris.com
> wolfgang.rumpf at gmail.com
> 
> Mobile - (614) 638-6797
> Skype - wolfgang.rumpf
> 
> 
> 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss

From wolfgang.rumpf at gmail.com  Wed Mar 16 10:11:26 2011
From: wolfgang.rumpf at gmail.com (Wolfgang Rumpf)
Date: Wed, 16 Mar 2011 10:11:26 -0400
Subject: [EMBOSS] Antwort:  Vienna in Emboss/Emboss-Explorer on Ubuntu?
In-Reply-To: <OF827F9BEE.E42D2CBA-ONC1257855.00331892-C1257855.0033C616@bayer.de>
References: <OF827F9BEE.E42D2CBA-ONC1257855.00331892-C1257855.0033C616@bayer.de>
Message-ID: <17E9EBB9-92C3-44E7-8CB8-381A32386982@gmail.com>

David, I suspected as much - I think my real concern is that I don't necessarily know the proper command-line syntax to control where the installation occurs.  My EMBOSS proper is in /usr/lib/emboss/; there appear to be additional files in /usr/share/emboss (e.g. acd, data, doc) and in /usr/share/emboss-explorer.  These should be the default locations for the packages from the Software Center in Ubuntu.

So given that, when I configure Vienna, do I tell Vienna that it will live in /usr/share/emboss by typing  ./configure --prefix=/usr/lib/emboss - or is there something I'm missing?


Wolfgang

Dr. Wolfgang Rumpf
Product Specialist, Rescentris Inc.
Adjunct Faculty, Dept. of Biotechnology, UMUC
--------------------------------------------------------
wolfgang.rumpf at rescentris.com
wolfgang.rumpf at gmail.com

Mobile - (614) 638-6797
Skype - wolfgang.rumpf



On Mar 16, 2011, at 5:25 AM, david.bauer at bayer.com wrote:

> 
> Hi, 
> 
> the emboss-explorer creates the html menu on the fly by calling the emboss program wossname. 
> So if you install the Vienna embassy package just in the same place like the main emboss, the vrnafold etc. should appear in the emboss-explorer. 
> But I'm not using it on Ubuntu so I do not know if there are any Ubuntu specific issues. 
> 
> HTH, 
> David. 
> 
> emboss-bounces at lists.open-bio.org schrieb am 15/03/2011 21:49:47:
> 
> > One of the ideas I try to teach in my bioinformatics class is RNA 
> > folding - and as such I'd love to add an RNA folding algorithm to my
> > bioinformatics server.  It seems like the "easiest" path might be 
> > Vienna since there's an EMBOSS port of it.  I'm not sure how to 
> > proceed, however - I've downloaded the source (VIENNA-1.7.2) and 
> > know the rough procedure for getting it installed, but I want it to 
> > "hook in" to my existing Ubuntu EMBOSS-Explorer (which is how my 
> > students access all of the other analyses we do).  Any ideas how to 
> > modify the installation to install to the correct path so that it 
> > will be available in my existing applications list?
> > 
> > Any help appreciated - thanks in advance!
> > 
> > 
> > Wolfgang
> > 
> > Dr. Wolfgang Rumpf
> > Product Specialist, Rescentris Inc.
> > Adjunct Faculty, Dept. of Biotechnology, UMUC
> > --------------------------------------------------------
> > wolfgang.rumpf at rescentris.com
> > wolfgang.rumpf at gmail.com
> > 
> > Mobile - (614) 638-6797
> > Skype - wolfgang.rumpf
> > 
> > 
> > 
> > 
> > _______________________________________________
> > EMBOSS mailing list
> > EMBOSS at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/emboss



From wolfgang.rumpf at gmail.com  Wed Mar 16 10:54:16 2011
From: wolfgang.rumpf at gmail.com (Wolfgang Rumpf)
Date: Wed, 16 Mar 2011 10:54:16 -0400
Subject: [EMBOSS] Antwort: Vienna in Emboss/Emboss-Explorer on Ubuntu?
In-Reply-To: <E6C88150E7007C4F8BA51F1F5DD4C0E9042FA3A341@UMMSCSMAIL01.ad.umassmed.edu>
References: <OF827F9BEE.E42D2CBA-ONC1257855.00331892-C1257855.0033C616@bayer.de>
	<17E9EBB9-92C3-44E7-8CB8-381A32386982@gmail.com>
	<E6C88150E7007C4F8BA51F1F5DD4C0E9042FA3A341@UMMSCSMAIL01.ad.umassmed.edu>
Message-ID: <899D5FD0-5211-40F7-9592-C65E108D887A@gmail.com>

I most certainly am HOPING to use the embassy package - that's the one I downloaded.  Again, is there any special command I need to use during the ./configure process in order to ensure that it goes into the correct locations (those corresponding to the locations where Emboss/Embassy were installed by the precompiled binaries from the Ubuntu Software Center)?  To clarify - I did NOT compile emboss/embassy myself; the Ubuntu Software Center installed those for me.  But now I want to add Vienna, and must do so by compiling, and I want it to "seamlessly" work with my existing Emboss/Embassy install....


Wolfgang

Dr. Wolfgang Rumpf
Product Specialist, Rescentris Inc.
Adjunct Faculty, Dept. of Biotechnology, UMUC
--------------------------------------------------------
wolfgang.rumpf at rescentris.com
wolfgang.rumpf at gmail.com

Mobile - (614) 638-6797
Skype - wolfgang.rumpf



On Mar 16, 2011, at 10:50 AM, Lapointe, David wrote:

> Are you using the embassy package for ViennaRNA? That compiles along with EMBOSS and ends up quite nicely with emboss-explorer. Use the software from here ftp://emboss.open-bio.org/pub/EMBOSS/  so the acd files are created.
> 
> David
> 
> --
> David Lapointe, Ph.D.
> Director Scientific Computing/Information Services
> University of Massachusetts Medical School
> 55 Lake Avenue N
> Worcester MA 01655
> 508-856-5141 (v)
> 
> 
> 
> -----Original Message-----
> From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Wolfgang Rumpf
> Sent: Wednesday, March 16, 2011 10:11 AM
> To: david.bauer at bayer.com
> Cc: emboss at lists.open-bio.org
> Subject: Re: [EMBOSS] Antwort: Vienna in Emboss/Emboss-Explorer on Ubuntu?
> 
> David, I suspected as much - I think my real concern is that I don't necessarily know the proper command-line syntax to control where the installation occurs.  My EMBOSS proper is in /usr/lib/emboss/; there appear to be additional files in /usr/share/emboss (e.g. acd, data, doc) and in /usr/share/emboss-explorer.  These should be the default locations for the packages from the Software Center in Ubuntu.
> 
> So given that, when I configure Vienna, do I tell Vienna that it will live in /usr/share/emboss by typing  ./configure --prefix=/usr/lib/emboss - or is there something I'm missing?
> 
> 
> Wolfgang
> 
> Dr. Wolfgang Rumpf
> Product Specialist, Rescentris Inc.
> Adjunct Faculty, Dept. of Biotechnology, UMUC
> --------------------------------------------------------
> wolfgang.rumpf at rescentris.com
> wolfgang.rumpf at gmail.com
> 
> Mobile - (614) 638-6797
> Skype - wolfgang.rumpf
> 
> 
> 
> On Mar 16, 2011, at 5:25 AM, david.bauer at bayer.com wrote:
> 
>> 
>> Hi, 
>> 
>> the emboss-explorer creates the html menu on the fly by calling the emboss program wossname. 
>> So if you install the Vienna embassy package just in the same place like the main emboss, the vrnafold etc. should appear in the emboss-explorer. 
>> But I'm not using it on Ubuntu so I do not know if there are any Ubuntu specific issues. 
>> 
>> HTH, 
>> David. 
>> 
>> emboss-bounces at lists.open-bio.org schrieb am 15/03/2011 21:49:47:
>> 
>>> One of the ideas I try to teach in my bioinformatics class is RNA 
>>> folding - and as such I'd love to add an RNA folding algorithm to my
>>> bioinformatics server.  It seems like the "easiest" path might be 
>>> Vienna since there's an EMBOSS port of it.  I'm not sure how to 
>>> proceed, however - I've downloaded the source (VIENNA-1.7.2) and 
>>> know the rough procedure for getting it installed, but I want it to 
>>> "hook in" to my existing Ubuntu EMBOSS-Explorer (which is how my 
>>> students access all of the other analyses we do).  Any ideas how to 
>>> modify the installation to install to the correct path so that it 
>>> will be available in my existing applications list?
>>> 
>>> Any help appreciated - thanks in advance!
>>> 
>>> 
>>> Wolfgang
>>> 
>>> Dr. Wolfgang Rumpf
>>> Product Specialist, Rescentris Inc.
>>> Adjunct Faculty, Dept. of Biotechnology, UMUC
>>> --------------------------------------------------------
>>> wolfgang.rumpf at rescentris.com
>>> wolfgang.rumpf at gmail.com
>>> 
>>> Mobile - (614) 638-6797
>>> Skype - wolfgang.rumpf
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
> 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
> 
> 



From david.bauer at bayer.com  Wed Mar 16 11:36:36 2011
From: david.bauer at bayer.com (david.bauer at bayer.com)
Date: Wed, 16 Mar 2011 16:36:36 +0100
Subject: [EMBOSS] Antwort: Re: Antwort: Vienna in Emboss/Emboss-Explorer on
	Ubuntu?
In-Reply-To: <899D5FD0-5211-40F7-9592-C65E108D887A@gmail.com>
Message-ID: <OF17552755.555B72AA-ONC1257855.0054F785-C1257855.0055C064@bayer.de>

Hi Wolfgang, 

mixing precompiled package installation with installations from source is 
dangerous and something one should never ever do.
In the normal emboss installation procedure (from source) you put the 
embassy packages within the source tree of emboss and run the compilation 
and installation from this place.
When I look at the directories you mention, where the emboss package is 
installed, this seems to be very ubuntu specific. So I hope someone who is 
familiar with ubuntu and/or the emboss package can help you with this.

David.

emboss-bounces at lists.open-bio.org schrieb am 16/03/2011 15:54:16:

> I most certainly am HOPING to use the embassy package - that's the 
> one I downloaded.  Again, is there any special command I need to use
> during the ./configure process in order to ensure that it goes into 
> the correct locations (those corresponding to the locations where 
> Emboss/Embassy were installed by the precompiled binaries from the 
> Ubuntu Software Center)?  To clarify - I did NOT compile 
> emboss/embassy myself; the Ubuntu Software Center installed those 
> for me.  But now I want to add Vienna, and must do so by compiling, 
> and I want it to "seamlessly" work with my existing Emboss/Embassy 
install....
> 
> 
> Wolfgang
> 
> Dr. Wolfgang Rumpf
> Product Specialist, Rescentris Inc.
> Adjunct Faculty, Dept. of Biotechnology, UMUC
> --------------------------------------------------------
> wolfgang.rumpf at rescentris.com
> wolfgang.rumpf at gmail.com
> 
> Mobile - (614) 638-6797
> Skype - wolfgang.rumpf
> 
> 
> 
> On Mar 16, 2011, at 10:50 AM, Lapointe, David wrote:
> 
> > Are you using the embassy package for ViennaRNA? That compiles 
> along with EMBOSS and ends up quite nicely with emboss-explorer. Use
> the software from here ftp://emboss.open-bio.org/pub/EMBOSS/  so the
> acd files are created.
> > 
> > David
> > 
> > --
> > David Lapointe, Ph.D.
> > Director Scientific Computing/Information Services
> > University of Massachusetts Medical School
> > 55 Lake Avenue N
> > Worcester MA 01655
> > 508-856-5141 (v)
> > 
> > 
> > 
> > -----Original Message-----
> > From: emboss-bounces at lists.open-bio.org [mailto:emboss-
> bounces at lists.open-bio.org] On Behalf Of Wolfgang Rumpf
> > Sent: Wednesday, March 16, 2011 10:11 AM
> > To: david.bauer at bayer.com
> > Cc: emboss at lists.open-bio.org
> > Subject: Re: [EMBOSS] Antwort: Vienna in Emboss/Emboss-Explorer on 
Ubuntu?
> > 
> > David, I suspected as much - I think my real concern is that I 
> don't necessarily know the proper command-line syntax to control 
> where the installation occurs.  My EMBOSS proper is in 
> /usr/lib/emboss/; there appear to be additional files in 
> /usr/share/emboss (e.g. acd, data, doc) and in /usr/share/emboss-
> explorer.  These should be the default locations for the packages 
> from the Software Center in Ubuntu.
> > 
> > So given that, when I configure Vienna, do I tell Vienna that it 
> will live in /usr/share/emboss by typing  ./configure --
> prefix=/usr/lib/emboss - or is there something I'm missing?
> > 
> > 
> > Wolfgang
> > 
> > Dr. Wolfgang Rumpf
> > Product Specialist, Rescentris Inc.
> > Adjunct Faculty, Dept. of Biotechnology, UMUC
> > --------------------------------------------------------
> > wolfgang.rumpf at rescentris.com
> > wolfgang.rumpf at gmail.com
> > 
> > Mobile - (614) 638-6797
> > Skype - wolfgang.rumpf
> > 
> > 
> > 
> > On Mar 16, 2011, at 5:25 AM, david.bauer at bayer.com wrote:
> > 
> >> 
> >> Hi, 
> >> 
> >> the emboss-explorer creates the html menu on the fly by calling 
> the emboss program wossname. 
> >> So if you install the Vienna embassy package just in the same 
> place like the main emboss, the vrnafold etc. should appear in the 
> emboss-explorer. 
> >> But I'm not using it on Ubuntu so I do not know if there are any 
> Ubuntu specific issues. 
> >> 
> >> HTH, 
> >> David. 
> >> 
> >> emboss-bounces at lists.open-bio.org schrieb am 15/03/2011 21:49:47:
> >> 
> >>> One of the ideas I try to teach in my bioinformatics class is RNA 
> >>> folding - and as such I'd love to add an RNA folding algorithm to my
> >>> bioinformatics server.  It seems like the "easiest" path might be 
> >>> Vienna since there's an EMBOSS port of it.  I'm not sure how to 
> >>> proceed, however - I've downloaded the source (VIENNA-1.7.2) and 
> >>> know the rough procedure for getting it installed, but I want it to 
> >>> "hook in" to my existing Ubuntu EMBOSS-Explorer (which is how my 
> >>> students access all of the other analyses we do).  Any ideas how to 
> >>> modify the installation to install to the correct path so that it 
> >>> will be available in my existing applications list?
> >>> 
> >>> Any help appreciated - thanks in advance!
> >>> 
> >>> 
> >>> Wolfgang
> >>> 
> >>> Dr. Wolfgang Rumpf
> >>> Product Specialist, Rescentris Inc.
> >>> Adjunct Faculty, Dept. of Biotechnology, UMUC
> >>> --------------------------------------------------------
> >>> wolfgang.rumpf at rescentris.com
> >>> wolfgang.rumpf at gmail.com
> >>> 
> >>> Mobile - (614) 638-6797
> >>> Skype - wolfgang.rumpf
> >>> 
> >>> 
> >>> 
> >>> 
> >>> _______________________________________________
> >>> EMBOSS mailing list
> >>> EMBOSS at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/emboss
> > 
> > 
> > _______________________________________________
> > EMBOSS mailing list
> > EMBOSS at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/emboss
> > 
> > 
> 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss

From stefanielager at gmail.com  Wed Mar 23 06:00:35 2011
From: stefanielager at gmail.com (Stefanie Lager)
Date: Wed, 23 Mar 2011 12:00:35 +0200
Subject: [EMBOSS] How to include homing endonucleases?
Message-ID: <AANLkTimVLvUKG1Y7ncZiCAQ-G5dv0ZavheBjqKBj5xiA@mail.gmail.com>

Hi,

Rebase got a separate file listing all homing  endonuclease
(ftp://ftp.neb.com/pub/rebase/homing.103), how can I index that file
as an alternative to rebase? The Emboss  program restrict have the
option to use a specific datafile, but it's not clear what format that
file should be?

Regards,

Stefanie Lager

From witch.of.agnessi at gmail.com  Wed Mar 23 16:46:01 2011
From: witch.of.agnessi at gmail.com (B Enn)
Date: Wed, 23 Mar 2011 16:46:01 -0400
Subject: [EMBOSS] the -orfminsize in SIXPACK and -minsize in GETORF
Message-ID: <AANLkTin5WfRdcC36QoLCi3namBzucV2b05fphAwD_FjR@mail.gmail.com>

Are the options -orfminsize in SIXPACK and -minsize in GETORF the same?

Do they both specify "Minimum nucleotide size of ORF to report"?

Are these two programs supposed to give the same results under identical
input parameters?

Thanks

From smehr at amnh.org  Thu Mar 31 17:14:33 2011
From: smehr at amnh.org (Shaadi Pooyaei Mehr)
Date: Thu, 31 Mar 2011 17:14:33 -0400
Subject: [EMBOSS] getorf executable
Message-ID: <019BC523-C8BB-422F-AE87-5AD4D728F55C@amnh.org>

Hi all, 

I have downloaded the EMBOSS 6.3.1 but the "getorf" executable is not part of it ! Do I need to get the separate CVS file? If so which one do I need to get?


Best


From hpm at bioinfo-user.org.uk  Wed Mar  2 09:25:05 2011
From: hpm at bioinfo-user.org.uk (Hamish McWilliam)
Date: Wed, 2 Mar 2011 09:25:05 +0000
Subject: [EMBOSS] accessing emboss ftp site
In-Reply-To: <AANLkTimGr7Y8ZKSRbqX87NN2_PHjF1BMWeyEVLAGQ=es@mail.gmail.com>
References: <6F57C2D1-8927-420C-940C-C6EC0C62AABE@gmail.com>
	<4BD0DB9B.5050005@sonsorol.org>
	<l2o5cba6b9f1004230756gf04316acq8519b375ce29e0d8@mail.gmail.com>
	<4BD1C05D.5010109@sonsorol.org>
	<FBBE6420-C5DA-4070-A67C-E7AC5A97F920@gmail.com>
	<AANLkTinK7fYE5U5uBmXiUaKh-BL61JI48WoRiRjlO9kD@mail.gmail.com>
	<4C50193D.5060500@bioteam.net>
	<AANLkTinGKTWZtj8EHBw1jmYnEO3X4Z2rQHSAM5OpE9KH@mail.gmail.com>
	<4C516A84.1050706@bioteam.net>
	<AANLkTimGr7Y8ZKSRbqX87NN2_PHjF1BMWeyEVLAGQ=es@mail.gmail.com>
Message-ID: <AANLkTinS_sS_6UMeVj2-hJRJE9XvzUvmmhHKzc+nooMR@mail.gmail.com>

Hi Chris,

You had any luck figuring out what is causing this issue with the FTP site?

Hamish

On 29 July 2010 14:46, Hamish McWilliam <hpm at bioinfo-user.org.uk> wrote:
> Hi Chris,
>
>> I did have to turn on support in VSFTPd for "ls -R" because it was
>> considered a possible resource drain or DOS target on large directories but
>> you are right that the extended mode passive stuff does not work. It does
>> not seem to be a firewall issue on the server and I don't think our upstream
>> Juniper SSG intrusion device is interfering.
>
> FWIW I get the same behavior when using passive or "active" FTP modes.
>
>> Can I ask what you are ?trying to accomplish? A mirror process? Can we get
>> around this problem via an anonymous RSYNC service pointing at the anonymous
>> FTP root? Passwordless SSH access for a mirror script that uses "rsync -avz
>> -e ssh ..." or similar?
>
> I'm trying to update the EMBL-EBI mirror of the EMBOSS software
> (ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/), this uses Mirror
> (ftp://ftp.ebi.ac.uk/pub/software/unix/mirror.tar.Z) to do the
> updates. As you can tell from the files in the directory this mirror
> no longer works, since it cannot get the listing of files. In fact it
> fails silently so I can't tell when the problem started.
>
>> vsftpd fits our needs for secure anonymous FTP server, if there is an easier
>> route to getting your needs sorted I might want to look at that rather than
>> going down deep into vsftp internals or swapping out the server software.
>
> From a few experiments with our vsftpd setup (CentOS 5.x, vsftpd
> 2.0.5) this looks to be supported by default, other than the -R thing.
>
> From a little Google it could be some interaction with the other
> components (http://www.ncftp.com/ncftpd/doc/misc/ftp_and_firewalls.html)
> where they don't recognize the FTP command correctly and choose the
> wrong mode, but it seems unlikely. Does it work if you run directly
> against the box?
>
> Hamish
>
>> Hamish McWilliam wrote:
>>>
>>> Hi Chris,
>>>
>>>> I can't seem to replicate this at all with any of my available FTP
>>>> clients
>>>> or browser-based FTP clients. It works for me from both Mac OS X clients
>>>> as
>>>> well as a CentOS 5.4 based Linux system.
>>>>
>>>> Is there an FTP client / OS combo that seems in particular not to work?
>>>
>>> This affects all clients I've tried.
>>>
>>> ?From your transcript, you are not running the commands required to see
>>> the issue:
>>>
>>> - 'ls' or 'dir' without options works
>>> - 'ls' or 'dir' with options hangs and eventually gives a timeout. FTP
>>> mirror systems often use -lRat as options to 'ls' to get all the files
>>> for a particular branch.
>>>
>>> $ ftp emboss.open-bio.org
>>> Connected to emboss.open-bio.org.
>>> 220 (vsFTPd 2.0.1)
>>> 530 Please login with USER and PASS.
>>> 530 Please login with USER and PASS.
>>> KERBEROS_V4 rejected as an authentication type
>>> Name (emboss.open-bio.org:hpm): ftp
>>> 331 Please specify the password.
>>> Password:
>>> 230 Login successful.
>>> Remote system type is UNIX.
>>> Using binary mode to transfer files.
>>> ftp> ?cd /pub/EMBOSS/fixes
>>> 250 Directory successfully changed.
>>> ftp> ?ls
>>> 227 Entering Passive Mode (208,94,50,58,51,71)
>>> 150 Here comes the directory listing.
>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ? ? 385 Jul 21 09:25 README.fixes
>>> -rwxrwxr-x ? ?1 501 ? ? ?503 ? ? ? ?506140 Jul 21 09:25 configure
>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ? ?5405 Jul 21 09:25 mysql.m4
>>> drwxrwsr-x ? ?4 501 ? ? ?503 ? ? ? ? ?4096 Jul 21 09:26 patches
>>> 226 Directory send OK.
>>> ftp> ?ls -lRat
>>> 227 Entering Passive Mode (208,94,50,58,31,88)
>>> *HANG*
>>>
>>> Compare with the equivalent session against the EMBL-EBI FTP site:
>>>
>>> $ ftp ftp.ebi.ac.uk
>>> Connected to ftp.ebi.ac.uk.
>>> 220-
>>> 220- ftp1.ebi.ac.uk FTP server
>>> 220-
>>> 220- WARNING: please note that the private part of this ftp service
>>> 220- has been migrated to ftp-private.ebi.ac.uk on 3rd June 2010.
>>> 220
>>> 530 Please login with USER and PASS.
>>> 530 Please login with USER and PASS.
>>> KERBEROS_V4 rejected as an authentication type
>>> Name (ftp.ebi.ac.uk:hpm): ftp
>>> 331 Please specify the password.
>>> Password:
>>> 230 Login successful.
>>> Remote system type is UNIX.
>>> Using binary mode to transfer files.
>>> ftp> ?cd /pub/software/unix/EMBOSS/fixes
>>> 250 Directory successfully changed.
>>> ftp> ?ls
>>> 227 Entering Passive Mode (193,62,193,4,238,107)
>>> 150 Here comes the directory listing.
>>> -r--r--r-- ? ?1 ftp ? ? ?ftp ? ? ? ? ? 180 Jan 15 ?2010 README.fixes
>>> 226 Directory send OK.
>>> ftp> ?ls -lRat
>>> 227 Entering Passive Mode (193,62,193,4,36,65)
>>> 150 Here comes the directory listing.
>>> .:
>>> drwxr-xr-x ? ?3 ftp ? ? ?ftp ? ? ? ? ?4096 Jan 18 ?2010 ..
>>> drwxr-xr-x ? ?2 ftp ? ? ?ftp ? ? ? ? ?4096 Jan 18 ?2010 .
>>> -r--r--r-- ? ?1 ftp ? ? ?ftp ? ? ? ? ? 180 Jan 15 ?2010 README.fixes
>>> 226 Directory send OK.
>>> ftp> ?bye
>>> 221 Goodbye.
>>>
>>> All the best,
>>>
>>> Hamish
>>>
>>>> Here is one example:
>>>>
>>>>> dag-static:~ dag$ ftp emboss.open-bio.org
>>>>> Connected to emboss.open-bio.org.
>>>>> 220 (vsFTPd 2.0.1)
>>>>> Name (emboss.open-bio.org:dag): anonymous
>>>>> 331 Please specify the password.
>>>>> Password:
>>>>> 230 Login successful.
>>>>> Remote system type is UNIX.
>>>>> Using binary mode to transfer files.
>>>>> ftp> ?dir
>>>>> 229 Entering Extended Passive Mode (|||54472|)
>>>>> 150 Here comes the directory listing.
>>>>> drwxr-xr-x ? ?8 14 ? ? ? 50 ? ? ? ? ? 4096 May 22 ?2006 pub
>>>>> 226 Directory send OK.
>>>>> ftp> ?cd pub/EMBOSS
>>>>> 250 Directory successfully changed.
>>>>> ftp> ?ls
>>>>> 229 Entering Extended Passive Mode (|||38343|)
>>>>> 150 Here comes the directory listing.
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?389856 Jul 21 09:25
>>>>> CBSTOOLS-1.0.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?426218 Jul 21 09:25
>>>>> DOMAINATRIX-0.1.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?441025 Jul 21 09:25
>>>>> DOMALIGN-0.1.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?452787 Jul 21 09:25
>>>>> DOMSEARCH-0.1.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ?23572243 Jul 19 13:41
>>>>> EMBOSS-6.3.1.tar.gz
>>>>> lrwxrwxrwx ? ?1 501 ? ? ?503 ? ? ? ? ? ?19 Jul 19 13:42
>>>>> EMBOSS-latest.tar.gz -> ?EMBOSS-6.3.1.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?373798 Jul 21 09:25 EMNU-1.05.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?415096 Jul 21 09:25
>>>>> ESIM4-1.0.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?569581 Jul 21 09:25
>>>>> HMMER-2.3.2.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?350791 Jul 21 09:25
>>>>> IPRSCAN-4.3.1.tar.gz
>>>>> drwxrwsr-x ? ?7 501 ? ? ?503 ? ? ? ? ?4096 Feb 01 ?2006 Jemboss
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?513418 Jul 21 09:25
>>>>> MEMENEW-4.0.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?823636 Jul 21 09:25
>>>>> MIRA-2.8.2.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?435315 Jul 21 09:25 MSE-3.0.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?328540 Jul 21 09:25
>>>>> MYEMBOSS-6.3.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?359488 Jul 21 09:25
>>>>> MYEMBOSSDEMO-6.3.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? 1667760 Jul 21 09:25
>>>>> PHYLIPNEW-3.69.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?571008 Jul 21 09:25
>>>>> SIGNATURE-0.1.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?531604 Jul 21 09:25
>>>>> STRUCTURE-0.1.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?386287 Jul 21 09:25
>>>>> TOPO-2.0.0.tar.gz
>>>>> -rw-rw-r-- ? ?1 501 ? ? ?503 ? ? ? ?652433 Jul 21 09:25
>>>>> VIENNA-1.7.2.tar.gz
>>>>> drwxrwsr-x ? ?3 522 ? ? ?503 ? ? ? ? ?4096 Aug 21 ?2006 contrib
>>>>> drwxrwsr-x ? ?2 501 ? ? ?503 ? ? ? ? ?4096 Nov 11 ?2005 doc
>>>>> drwxrwsr-x ? ?3 501 ? ? ?503 ? ? ? ? ?4096 Jul 21 09:25 fixes
>>>>> drwxrwsr-x ? 14 501 ? ? ?503 ? ? ? ? ?4096 Jul 19 13:39 old
>>>>> drwxrwsr-x ? ?2 501 ? ? ?503 ? ? ? ? ?4096 Jul 06 ?2005 tutorials
>>>>> drwxrwsr-x ? ?4 501 ? ? ?503 ? ? ? ? ?4096 Jul 19 13:36 windows
>>>>> 226 Directory send OK.
>>>>> ftp>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Hamish McWilliam wrote:
>>>>>
>>>>> Hi Chris,
>>>>>
>>>>> I'm also seeing problems with the FTP site, but using Mirror rather
>>>>> than Transmit, it looks like the server does not like options being
>>>>> specified to the LIST command:
>>>>>
>>>>> Scanning remote directory /pub/EMBOSS
>>>>> ---> ? ?CWD /pub/EMBOSS
>>>>> 250 Directory successfully changed.
>>>>> ---> ? ?TYPE A
>>>>> 200 Switching to ASCII mode.
>>>>> ---> ? ?PORT 172,21,22,1,171,245
>>>>> 200 PORT command successful. Consider using PASV.
>>>>> ---> ? ?PASV
>>>>> 227 Entering Passive Mode (208,94,50,58,104,178)
>>>>> ---> ? ?LIST -lat
>>>>> timed out
>>>>> Cannot get remote directory listing because: timed out
>>>>> Cannot get remote directory details (/pub/EMBOSS)
>>>>> disconnecting from emboss.open-bio.org
>>>>>
>>>>> Trying it with a command line client I get the response to hang if I
>>>>> try using any options to ls or dir, without options they are fine.
>>>>>
>>>>> All the best,
>>>>>
>>>>> Hamish
>>>>>
>>>>> On 29 May 2010 03:44, Koen van der Drift<koenvanderdrift at gmail.com>
>>>>> ?wrote:
>>>>>>
>>>>>> Hi Chris,
>>>>>>
>>>>>> Did you have a chance to look at this? Just tried again, and Transmit
>>>>>> still
>>>>>> won't let me access the emboss ftp site.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> - Koen.
>>>>>>
>>>>>>
>>>>>> On Apr 23, 2010, at 11:44 AM, Chris Dagdigian wrote:
>>>>>>
>>>>>>> In the last few months the open-bio.org servers switched datacenters,
>>>>>>> IP
>>>>>>> addresses and firewall/IDS appliances. Lots of juicy things to look at
>>>>>>> and
>>>>>>> debug.
>>>>>>>
>>>>>>> Koen - if you have a chance can you send me the IP address that you
>>>>>>> are
>>>>>>> using to connect from? I might be able to find some relevant log
>>>>>>> entries
>>>>>>> with that info.
>>>>>>>
>>>>>>> -Chris
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Koen van der Drift wrote:
>>>>>>>>
>>>>>>>> Just for the record, it used to work with Transmit, this is only from
>>>>>>>> the last few months.
>>>>>>>>
>>>>>>>> - Koen.
>>>>>>>>
>>>>>>>> On Thu, Apr 22, 2010 at 7:28 PM, Chris Dagdigian<dag at sonsorol.org>
>>>>>>>> ?wrote:
>>>>>>>>>
>>>>>>>>> Might be an issue with the Juniper Netscreen firewall/IDS security
>>>>>>>>> appliance
>>>>>>>>> that sits upstream of the EMBOSS FTP server. I'll take a look at the
>>>>>>>>> security logs and alerts.
>>>>>>>>>
>>>>>>>>> -Chris
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Koen van der Drift wrote:
>>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> For a while now I am unable to access the emboss ftp site using the
>>>>>>>>>> OS
>>>>>>>>>> X
>>>>>>>>>> client Transmit. Loggin in works fine, but it chokes on the LIST
>>>>>>>>>> command. I have no problems accessing it from the command line. I
>>>>>>>>>> have
>>>>>>>>>> added the output from Transmit below. I don't know if this is a
>>>>>>>>>> Transmit
>>>>>>>>>> or emboss issue, but just wanted to let you know.
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> - Koen.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Transmit 3.6.9 Session Transcript
>>>>>>>>>> LibNcFTP 3.2.1 (August 13, 2007) compiled for UNIX
>>>>>>>>>> Uname: Darwin|exile.local|9.8.0|Darwin Kernel Version 9.8.0: Wed
>>>>>>>>>> Jul
>>>>>>>>>> 15
>>>>>>>>>> 16:57:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_PPC|Power Macintosh
>>>>>>>>>> 220: (vsFTPd 2.0.1)
>>>>>>>>>> Connected to emboss.open-bio.org.
>>>>>>>>>> Cmd: USER anonymous
>>>>>>>>>> 331: Please specify the password.
>>>>>>>>>> Cmd: PASS NcFTP@
>>>>>>>>>> 230: Login successful.
>>>>>>>>>> Cmd: TYPE A
>>>>>>>>>> 200: Switching to ASCII mode.
>>>>>>>>>> Logged in to emboss.open-bio.org as anonymous.
>>>>>>>>>> Cmd: SYST
>>>>>>>>>> 215: UNIX Type: L8
>>>>>>>>>> Cmd: PWD
>>>>>>>>>> 257: "/"
>>>>>>>>>> Cmd: CWD /pub/EMBOSS/fixes
>>>>>>>>>> 250: Directory successfully changed.
>>>>>>>>>> Cmd: PWD
>>>>>>>>>> 257: "/pub/EMBOSS/fixes"
>>>>>>>>>> Cmd: PASV
>>>>>>>>>> 227: Entering Passive Mode (208,94,50,58,83,232)
>>>>>>>>>> Cmd: LIST -a
>>>>>>>>>> Could not read reply from control connection -- timed out.
>>>>>>>>>> (SReadline
>>>>>>>>>> 1)
>>>>>>>>>> 220: (vsFTPd 2.0.1)
>>>>>>>>>> Connected to emboss.open-bio.org.
>>>>>>>>>> Cmd: USER anonymous
>>>>>>>>>> 331: Please specify the password.
>>>>>>>>>> Cmd: PASS NcFTP@
>>>>>>>>>> 230: Login successful.
>>>>>>>>>> Logged in to emboss.open-bio.org as anonymous.
>>>>>>>>>> Cmd: SYST
>>>>>>>>>> 215: UNIX Type: L8
>>>>>>>>>> Cmd: PWD
>>>>>>>>>> 257: "/"
>>>>>>>>>> Cmd: CWD /pub/EMBOSS/fixes
>>>>>>>>>> 250: Directory successfully changed.
>>>>>>>>>> Cmd: PWD
>>>>>>>>>> 257: "/pub/EMBOSS/fixes"
>>>>>>>>>> Cmd: PASV
>>>>>>>>>> 227: Entering Passive Mode (208,94,50,58,222,100)
>>>>>>>>>> Cmd: LIST -a
>>>>>>>>>> Could not read reply from control connection -- timed out.
>>>>>>>>>> (SReadline
>>>>>>>>>> 1)
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> EMBOSS mailing list
>>>>>>>>>> EMBOSS at lists.open-bio.org
>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>>>>
>>>>>> _______________________________________________
>>>>>> EMBOSS mailing list
>>>>>> EMBOSS at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>>>>
>>>>>
>>>>>
>>>
>>>
>>>
>>
>
>
>
> --
> ----
> "Saying the internet has changed dramatically over the last five years
> is clich? ? the internet is always changing dramatically" - Craig
> Labovitz, Arbor Networks.
>



-- 
----
"Saying the internet has changed dramatically over the last five years
is clich? ? the internet is always changing dramatically" - Craig
Labovitz, Arbor Networks.



From wolfgang.rumpf at rescentris.com  Wed Mar  9 20:00:41 2011
From: wolfgang.rumpf at rescentris.com (Wolfgang Rumpf)
Date: Wed, 9 Mar 2011 15:00:41 -0500
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
	ajSeqdbInit
Message-ID: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>

I have an Emboss installation I'm using for teaching purposes.  It was
working just fine until a few days ago, when I updated my OS to Ubuntu 10.10
(from 10.4).  Now I'm getting this error, specifically when I run fdnapars.
I'm worried that more might be broken, and I can't find anything useful via
google when I search for the error.  Can anyone shed some light on what's
going on here?

fdnapars: symbol lookup error: /usr/lib/libnucleus.so.6: undefined
symbol: ajSeqdbInit



Cheers,

Wolfgang

----------------------
Wolfgang Rumpf, Ph.D.
Product Specialist, Rescentris Inc
Adjunct Faculty, UMUC Dept. of Biotechnology
----------------------


From egorleg at gmail.com  Wed Mar  9 23:10:13 2011
From: egorleg at gmail.com (Kevin Egan)
Date: Wed, 9 Mar 2011 23:10:13 +0000
Subject: [EMBOSS] HELP! DOTMATCHER
Message-ID: <AANLkTin38ZwuTepHrf8MU8RsBhOXBOfvWDHLoFOQwq6B@mail.gmail.com>

Hi

I entered the information as follows

dotmatcher -asequence cam3.txt -bsequence TCH3A.txt [-matrixfile EDNAFULL]
[-windowsize 10] [-threshold 70]

but got a 'too many parameters' error message.

Does anyone know how to enter my own values for window length etc?

Regards,

Kevin


From idrummon at receptor.mgh.harvard.edu  Wed Mar  9 23:31:24 2011
From: idrummon at receptor.mgh.harvard.edu (Iain Drummond)
Date: Wed, 09 Mar 2011 18:31:24 -0500
Subject: [EMBOSS] HELP! DOTMATCHER
In-Reply-To: <AANLkTin38ZwuTepHrf8MU8RsBhOXBOfvWDHLoFOQwq6B@mail.gmail.com>
Message-ID: <C99D77FC.1F2B%idrummon@receptor.mgh.harvard.edu>

Hi Kevin,

For starters i would get rid of the square brackets ("[]") in your command;
i don't think these are necessary.

Iain Drummond


On 3/9/11 6:10 PM, "Kevin Egan" <egorleg at gmail.com> wrote:

> Hi
> 
> I entered the information as follows
> 
> dotmatcher -asequence cam3.txt -bsequence TCH3A.txt [-matrixfile EDNAFULL]
> [-windowsize 10] [-threshold 70]
> 
> but got a 'too many parameters' error message.
> 
> Does anyone know how to enter my own values for window length etc?
> 
> Regards,
> 
> Kevin
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
> 




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From marvin.stodolsky at gmail.com  Thu Mar 10 00:48:41 2011
From: marvin.stodolsky at gmail.com (Marvin Stodolsky)
Date: Wed, 9 Mar 2011 19:48:41 -0500
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
	ajSeqdbInit
In-Reply-To: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>
Message-ID: <AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>

Wolfgang

RE:  undefined symbol: ajSeqdbInit
While not an expert at all, on Emboss code,
this type of error is typically due to (Emboss) binaries Not Yet
being compiled with the newer linux-header resources.  Pending that
compilation by the Emboss maintenance team, if you run the compile
from Emboss source code on your own  Ubuntu 10.10 system, all will
likely be  OK.

Check if linux-headers are installed on your System with:
$ sudo apt-get update
$ sudo apt-get install linux-headers-$(uname -r)

You could also just reinstall and boot under the last kernel supporting Emboss.
Typically linux is backward compatible to prior kernels, for a
considerable period.
Just search out the prior linux-image package at: http://packages.ubuntu.com

MarvS
scanModem maintainer



On Wed, Mar 9, 2011 at 3:00 PM, Wolfgang Rumpf
<wolfgang.rumpf at rescentris.com> wrote:
> I have an Emboss installation I'm using for teaching purposes. ?It was
> working just fine until a few days ago, when I updated my OS to Ubuntu 10.10
> (from 10.4). ?Now I'm getting this error, specifically when I run fdnapars.
> I'm worried that more might be broken, and I can't find anything useful via
> google when I search for the error. ?Can anyone shed some light on what's
> going on here?
>
> fdnapars: symbol lookup error: /usr/lib/libnucleus.so.6: undefined
> symbol: ajSeqdbInit
>
>
>
> Cheers,
>
> Wolfgang
>
> ----------------------
> Wolfgang Rumpf, Ph.D.
> Product Specialist, Rescentris Inc
> Adjunct Faculty, UMUC Dept. of Biotechnology
> ----------------------
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From pmr at ebi.ac.uk  Thu Mar 10 01:00:56 2011
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 10 Mar 2011 01:00:56 +0000
Subject: [EMBOSS] HELP! DOTMATCHER
In-Reply-To: <C99D77FC.1F2B%idrummon@receptor.mgh.harvard.edu>
References: <C99D77FC.1F2B%idrummon@receptor.mgh.harvard.edu>
Message-ID: <4D7822C8.6040309@ebi.ac.uk>

On 09/03/2011 23:31, Iain Drummond wrote:
> Hi Kevin,
>
> For starters i would get rid of the square brackets ("[]") in your command;
> i don't think these are necessary.

That's the right answer. Qualifiers on the command line must start with 
'-' otherwise they are counted as 'parameters'. The square brackets are 
hiding the crucial dashes.

regards,

Peter Rice
EMBOSS Team

> On 3/9/11 6:10 PM, "Kevin Egan"<egorleg at gmail.com>  wrote:
>
>> Hi
>>
>> I entered the information as follows
>>
>> dotmatcher -asequence cam3.txt -bsequence TCH3A.txt [-matrixfile EDNAFULL]
>> [-windowsize 10] [-threshold 70]
>>
>> but got a 'too many parameters' error message.


From charles-listes-emboss at plessy.org  Thu Mar 10 01:37:00 2011
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Thu, 10 Mar 2011 10:37:00 +0900
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
 ajSeqdbInit
In-Reply-To: <AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>
	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>
Message-ID: <20110310013700.GC11010@merveille.plessy.net>

Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a ?crit :
> 
> RE:  undefined symbol: ajSeqdbInit
> While not an expert at all, on Emboss code,
> this type of error is typically due to (Emboss) binaries Not Yet
> being compiled with the newer linux-header resources.  Pending that
> compilation by the Emboss maintenance team, if you run the compile
> from Emboss source code on your own  Ubuntu 10.10 system, all will
> likely be  OK.

Dear Wolfgang,

you can also give a try to the emboss and embassy-phylip from 11.04 Ubuntu
distribution. If you can install them on 10.10, they should work well, and
they are up to date.

http://packages.ubuntu.com/natty/emboss
http://packages.ubuntu.com/natty/embassy-phylip

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


From wolfgang.rumpf at rescentris.com  Thu Mar 10 15:26:38 2011
From: wolfgang.rumpf at rescentris.com (Wolfgang Rumpf)
Date: Thu, 10 Mar 2011 10:26:38 -0500
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
	ajSeqdbInit
In-Reply-To: <20110310013700.GC11010@merveille.plessy.net>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>
	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>
	<20110310013700.GC11010@merveille.plessy.net>
Message-ID: <BD9C610C-7ADE-4D73-9094-94CE5DFD1F50@mac.com>

So as I understand it my options are:

1.  Boot with an older kernel - probably the latest one from 10.4, if it works with 10.10;
2.  Recompile EMBOSS myself;
3.  Download and install the 11.04 (unreleased) Emboss/Embassy installs;
4.  Wait for 11.04 to come out 

Of all of these the "simplest" (other than just waiting) would probably be to try to boot with an older kernel - I don't want to bring the rest of the EMBOSS system down for an extended time period, perhaps very extended if the compilation/install doesn't go as planned.

Sound about right?

Wolfgang

Dr. Wolfgang Rumpf
Product Specialist, Rescentris Inc.
--------------------------------------------------------
wolfgang.rumpf at rescentris.com

Mobile - (614) 638-6797
Skype - wolfgang.rumpf




On Mar 9, 2011, at 8:37 PM, Charles Plessy wrote:

> Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a ?crit :
>> 
>> RE:  undefined symbol: ajSeqdbInit
>> While not an expert at all, on Emboss code,
>> this type of error is typically due to (Emboss) binaries Not Yet
>> being compiled with the newer linux-header resources.  Pending that
>> compilation by the Emboss maintenance team, if you run the compile
>> from Emboss source code on your own  Ubuntu 10.10 system, all will
>> likely be  OK.
> 
> Dear Wolfgang,
> 
> you can also give a try to the emboss and embassy-phylip from 11.04 Ubuntu
> distribution. If you can install them on 10.10, they should work well, and
> they are up to date.
> 
> http://packages.ubuntu.com/natty/emboss
> http://packages.ubuntu.com/natty/embassy-phylip
> 
> Have a nice day,
> 
> -- 
> Charles Plessy
> Debian Med packaging team
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss




From marvin.stodolsky at gmail.com  Thu Mar 10 17:58:37 2011
From: marvin.stodolsky at gmail.com (Marvin Stodolsky)
Date: Thu, 10 Mar 2011 12:58:37 -0500
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
	ajSeqdbInit
In-Reply-To: <BD9C610C-7ADE-4D73-9094-94CE5DFD1F50@mac.com>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>
	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>
	<20110310013700.GC11010@merveille.plessy.net>
	<BD9C610C-7ADE-4D73-9094-94CE5DFD1F50@mac.com>
Message-ID: <AANLkTimOW9i0hbmo2RPuhOCE8RnGNZ08dVH7=QxP5NNU@mail.gmail.com>

Wolfgang

> 1.  Boot with an older kernel - probably the latest one from 10.4, if it works with 10.10;
really is expected to be trouble free.  Linux strives to maintain
backward compatibility.

In the course of aiding modem users, I have and boot with numerous
older kernels on my Systems.
Your worst case scenario is that a bootup with an older kernel will
fail.  Then you will have to reboot with the current one. Merely
having an older kernel installed will IN NO WAY interfere with usage
of more recent kernels.

Marvin

On Thu, Mar 10, 2011 at 10:26 AM, Wolfgang Rumpf
<wolfgang.rumpf at rescentris.com> wrote:
> So as I understand it my options are:
>
> 1. ?Boot with an older kernel - probably the latest one from 10.4, if it works with 10.10;
> 2. ?Recompile EMBOSS myself;
> 3. ?Download and install the 11.04 (unreleased) Emboss/Embassy installs;
> 4. ?Wait for 11.04 to come out
>
> Of all of these the "simplest" (other than just waiting) would probably be to try to boot with an older kernel - I don't want to bring the rest of the EMBOSS system down for an extended time period, perhaps very extended if the compilation/install doesn't go as planned.
>
> Sound about right?
>
> Wolfgang
>
> Dr. Wolfgang Rumpf
> Product Specialist, Rescentris Inc.
> --------------------------------------------------------
> wolfgang.rumpf at rescentris.com
>
> Mobile - (614) 638-6797
> Skype - wolfgang.rumpf
>
>
>
>
> On Mar 9, 2011, at 8:37 PM, Charles Plessy wrote:
>
>> Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a ?crit :
>>>
>>> RE: ?undefined symbol: ajSeqdbInit
>>> While not an expert at all, on Emboss code,
>>> this type of error is typically due to (Emboss) binaries Not Yet
>>> being compiled with the newer linux-header resources. ?Pending that
>>> compilation by the Emboss maintenance team, if you run the compile
>>> from Emboss source code on your own ?Ubuntu 10.10 system, all will
>>> likely be ?OK.
>>
>> Dear Wolfgang,
>>
>> you can also give a try to the emboss and embassy-phylip from 11.04 Ubuntu
>> distribution. If you can install them on 10.10, they should work well, and
>> they are up to date.
>>
>> http://packages.ubuntu.com/natty/emboss
>> http://packages.ubuntu.com/natty/embassy-phylip
>>
>> Have a nice day,
>>
>> --
>> Charles Plessy
>> Debian Med packaging team
>> http://www.debian.org/devel/debian-med
>> Tsurumi, Kanagawa, Japan
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From henrikki.almusa at helsinki.fi  Thu Mar 10 18:27:42 2011
From: henrikki.almusa at helsinki.fi (Henrikki Almusa)
Date: Thu, 10 Mar 2011 20:27:42 +0200
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error
	-	ajSeqdbInit
In-Reply-To: <BD9C610C-7ADE-4D73-9094-94CE5DFD1F50@mac.com>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>	<20110310013700.GC11010@merveille.plessy.net>
	<BD9C610C-7ADE-4D73-9094-94CE5DFD1F50@mac.com>
Message-ID: <4D79181E.1050007@helsinki.fi>

On 2011-03-10 17:26, Wolfgang Rumpf wrote:
> So as I understand it my options are:
>
> 1.  Boot with an older kernel - probably the latest one from 10.4, if it works with 10.10;
> 2.  Recompile EMBOSS myself;
> 3.  Download and install the 11.04 (unreleased) Emboss/Embassy installs;
> 4.  Wait for 11.04 to come out
>
> Of all of these the "simplest" (other than just waiting) would probably be to try to boot with an older kernel - I don't want to bring the rest of the EMBOSS system down for an extended time period, perhaps very extended if the compilation/install doesn't go as planned.
>
> Sound about right?

The error message complains about missing library file libnucleus.so.6 
which was probably removed in update as there was no dependency on it 
(within the package lists). So here's a way to fix it:
  - go to packages.ubuntu.com and search for a package with file called 
libnucleus.so.6
  - get result which tells you that it is in package libnucleus6
  - install that named package with your favourite tool (for example 
apt-get)


> Wolfgang
>
> Dr. Wolfgang Rumpf
> Product Specialist, Rescentris Inc.
> --------------------------------------------------------
> wolfgang.rumpf at rescentris.com
>
> Mobile - (614) 638-6797
> Skype - wolfgang.rumpf
>
>
>
>
> On Mar 9, 2011, at 8:37 PM, Charles Plessy wrote:
>
>> Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a ?crit :
>>>
>>> RE:  undefined symbol: ajSeqdbInit
>>> While not an expert at all, on Emboss code,
>>> this type of error is typically due to (Emboss) binaries Not Yet
>>> being compiled with the newer linux-header resources.  Pending that
>>> compilation by the Emboss maintenance team, if you run the compile
>>> from Emboss source code on your own  Ubuntu 10.10 system, all will
>>> likely be  OK.
>>
>> Dear Wolfgang,
>>
>> you can also give a try to the emboss and embassy-phylip from 11.04 Ubuntu
>> distribution. If you can install them on 10.10, they should work well, and
>> they are up to date.
>>
>> http://packages.ubuntu.com/natty/emboss
>> http://packages.ubuntu.com/natty/embassy-phylip
>>
>> Have a nice day,
>>
>> --
>> Charles Plessy
>> Debian Med packaging team
>> http://www.debian.org/devel/debian-med
>> Tsurumi, Kanagawa, Japan
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>


-- 
Henrikki Almusa



From marvin.stodolsky at gmail.com  Thu Mar 10 23:48:46 2011
From: marvin.stodolsky at gmail.com (Marvin Stodolsky)
Date: Thu, 10 Mar 2011 18:48:46 -0500
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
	ajSeqdbInit
In-Reply-To: <4D79181E.1050007@helsinki.fi>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>
	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>
	<20110310013700.GC11010@merveille.plessy.net>
	<BD9C610C-7ADE-4D73-9094-94CE5DFD1F50@mac.com>
	<4D79181E.1050007@helsinki.fi>
Message-ID: <AANLkTikYZuk8mypJ5_MteeO0tCE2wtGbphM2wVpGrXK+@mail.gmail.com>

There is a:
http://packages.ubuntu.com/maverick/libnucleus6

$ sudo apt-get update
$ sudo apt-get libnucleus6

should do all necessary.

MarvS

On Thu, Mar 10, 2011 at 1:27 PM, Henrikki Almusa
<henrikki.almusa at helsinki.fi> wrote:
> On 2011-03-10 17:26, Wolfgang Rumpf wrote:
>>
>> So as I understand it my options are:
>>
>> 1. ?Boot with an older kernel - probably the latest one from 10.4, if it
>> works with 10.10;
>> 2. ?Recompile EMBOSS myself;
>> 3. ?Download and install the 11.04 (unreleased) Emboss/Embassy installs;
>> 4. ?Wait for 11.04 to come out
>>
>> Of all of these the "simplest" (other than just waiting) would probably be
>> to try to boot with an older kernel - I don't want to bring the rest of the
>> EMBOSS system down for an extended time period, perhaps very extended if the
>> compilation/install doesn't go as planned.
>>
>> Sound about right?
>
> The error message complains about missing library file libnucleus.so.6 which
> was probably removed in update as there was no dependency on it (within the
> package lists). So here's a way to fix it:
> ?- go to packages.ubuntu.com and search for a package with file called
> libnucleus.so.6
> ?- get result which tells you that it is in package libnucleus6
> ?- install that named package with your favourite tool (for example apt-get)
>
>
>> Wolfgang
>>
>> Dr. Wolfgang Rumpf
>> Product Specialist, Rescentris Inc.
>> --------------------------------------------------------
>> wolfgang.rumpf at rescentris.com
>>
>> Mobile - (614) 638-6797
>> Skype - wolfgang.rumpf
>>
>>
>>
>>
>> On Mar 9, 2011, at 8:37 PM, Charles Plessy wrote:
>>
>>> Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a ?crit :
>>>>
>>>> RE: ?undefined symbol: ajSeqdbInit
>>>> While not an expert at all, on Emboss code,
>>>> this type of error is typically due to (Emboss) binaries Not Yet
>>>> being compiled with the newer linux-header resources. ?Pending that
>>>> compilation by the Emboss maintenance team, if you run the compile
>>>> from Emboss source code on your own ?Ubuntu 10.10 system, all will
>>>> likely be ?OK.
>>>
>>> Dear Wolfgang,
>>>
>>> you can also give a try to the emboss and embassy-phylip from 11.04
>>> Ubuntu
>>> distribution. If you can install them on 10.10, they should work well,
>>> and
>>> they are up to date.
>>>
>>> http://packages.ubuntu.com/natty/emboss
>>> http://packages.ubuntu.com/natty/embassy-phylip
>>>
>>> Have a nice day,
>>>
>>> --
>>> Charles Plessy
>>> Debian Med packaging team
>>> http://www.debian.org/devel/debian-med
>>> Tsurumi, Kanagawa, Japan
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>
>
> --
> Henrikki Almusa
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From wolfgang.rumpf at gmail.com  Fri Mar 11 02:24:07 2011
From: wolfgang.rumpf at gmail.com (Wolfgang Rumpf)
Date: Thu, 10 Mar 2011 21:24:07 -0500
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
	ajSeqdbInit
In-Reply-To: <AANLkTikYZuk8mypJ5_MteeO0tCE2wtGbphM2wVpGrXK+@mail.gmail.com>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>	<20110310013700.GC11010@merveille.plessy.net>	<BD9C610C-7ADE-4D73-9094-94CE5DFD1F50@mac.com>	<4D79181E.1050007@helsinki.fi>
	<AANLkTikYZuk8mypJ5_MteeO0tCE2wtGbphM2wVpGrXK+@mail.gmail.com>
Message-ID: <4D7987C7.7020501@gmail.com>

Everything I have tried has failed.   I have uninstalled and reinstalled 
the entire EMBOSS/EMBASSY suite.  I have booted from the previous 
kernel.  Recompilation is a bit beyond me, I fear - what are the chances 
that this will just be fixed when 11.04 rolls out?  Has anyone else had 
this problem?

What's perplexing is that this has happened on both of my Ubuntu 
systems; there's nothing that was caused by me "tinkering" - this 
happened after the update to 10.10.  Why didn't this get caught - am I 
the only person using Phylip in Emboss Explorer?

On 03/10/2011 06:48 PM, Marvin Stodolsky wrote:
> There is a:
> http://packages.ubuntu.com/maverick/libnucleus6
>
> $ sudo apt-get update
> $ sudo apt-get libnucleus6
>
> should do all necessary.
>
> MarvS
>
> On Thu, Mar 10, 2011 at 1:27 PM, Henrikki Almusa
> <henrikki.almusa at helsinki.fi>  wrote:
>> On 2011-03-10 17:26, Wolfgang Rumpf wrote:
>>> So as I understand it my options are:
>>>
>>> 1.  Boot with an older kernel - probably the latest one from 10.4, if it
>>> works with 10.10;
>>> 2.  Recompile EMBOSS myself;
>>> 3.  Download and install the 11.04 (unreleased) Emboss/Embassy installs;
>>> 4.  Wait for 11.04 to come out
>>>
>>> Of all of these the "simplest" (other than just waiting) would probably be
>>> to try to boot with an older kernel - I don't want to bring the rest of the
>>> EMBOSS system down for an extended time period, perhaps very extended if the
>>> compilation/install doesn't go as planned.
>>>
>>> Sound about right?
>> The error message complains about missing library file libnucleus.so.6 which
>> was probably removed in update as there was no dependency on it (within the
>> package lists). So here's a way to fix it:
>>   - go to packages.ubuntu.com and search for a package with file called
>> libnucleus.so.6
>>   - get result which tells you that it is in package libnucleus6
>>   - install that named package with your favourite tool (for example apt-get)
>>
>>
>>> Wolfgang
>>>
>>> Dr. Wolfgang Rumpf
>>> Product Specialist, Rescentris Inc.
>>> --------------------------------------------------------
>>> wolfgang.rumpf at rescentris.com
>>>
>>> Mobile - (614) 638-6797
>>> Skype - wolfgang.rumpf
>>>
>>>
>>>
>>>
>>> On Mar 9, 2011, at 8:37 PM, Charles Plessy wrote:
>>>
>>>> Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a ?crit :
>>>>> RE:  undefined symbol: ajSeqdbInit
>>>>> While not an expert at all, on Emboss code,
>>>>> this type of error is typically due to (Emboss) binaries Not Yet
>>>>> being compiled with the newer linux-header resources.  Pending that
>>>>> compilation by the Emboss maintenance team, if you run the compile
>>>>> from Emboss source code on your own  Ubuntu 10.10 system, all will
>>>>> likely be  OK.
>>>> Dear Wolfgang,
>>>>
>>>> you can also give a try to the emboss and embassy-phylip from 11.04
>>>> Ubuntu
>>>> distribution. If you can install them on 10.10, they should work well,
>>>> and
>>>> they are up to date.
>>>>
>>>> http://packages.ubuntu.com/natty/emboss
>>>> http://packages.ubuntu.com/natty/embassy-phylip
>>>>
>>>> Have a nice day,
>>>>
>>>> --
>>>> Charles Plessy
>>>> Debian Med packaging team
>>>> http://www.debian.org/devel/debian-med
>>>> Tsurumi, Kanagawa, Japan
>>>> _______________________________________________
>>>> EMBOSS mailing list
>>>> EMBOSS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>
>>
>> --
>> Henrikki Almusa
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss



From wolfgang.rumpf at gmail.com  Fri Mar 11 02:26:44 2011
From: wolfgang.rumpf at gmail.com (Wolfgang Rumpf)
Date: Thu, 10 Mar 2011 21:26:44 -0500
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
	ajSeqdbInit
In-Reply-To: <20110310013700.GC11010@merveille.plessy.net>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>
	<20110310013700.GC11010@merveille.plessy.net>
Message-ID: <4D798864.9090801@gmail.com>

Also tried and failed - apparently there were dependencies that couldn't 
be resolved.

On 03/09/2011 08:37 PM, Charles Plessy wrote:
> Le Wed, Mar 09, 2011 at 07:48:41PM -0500, Marvin Stodolsky a ?crit :
>> RE:  undefined symbol: ajSeqdbInit
>> While not an expert at all, on Emboss code,
>> this type of error is typically due to (Emboss) binaries Not Yet
>> being compiled with the newer linux-header resources.  Pending that
>> compilation by the Emboss maintenance team, if you run the compile
>> from Emboss source code on your own  Ubuntu 10.10 system, all will
>> likely be  OK.
> Dear Wolfgang,
>
> you can also give a try to the emboss and embassy-phylip from 11.04 Ubuntu
> distribution. If you can install them on 10.10, they should work well, and
> they are up to date.
>
> http://packages.ubuntu.com/natty/emboss
> http://packages.ubuntu.com/natty/embassy-phylip
>
> Have a nice day,
>



From charles-listes-emboss at plessy.org  Fri Mar 11 15:54:06 2011
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Sat, 12 Mar 2011 00:54:06 +0900
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
 ajSeqdbInit
In-Reply-To: <4D798864.9090801@gmail.com>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>
	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>
	<20110310013700.GC11010@merveille.plessy.net>
	<4D798864.9090801@gmail.com>
Message-ID: <20110311155406.GQ2316@merveille.plessy.net>

Le Thu, Mar 10, 2011 at 09:26:44PM -0500, Wolfgang Rumpf a ?crit :
> Also tried and failed - apparently there were dependencies that
> couldn't be resolved.

I have prepared unofficial backports of EMBOSS 6.3.1 and EMBASSY-PHYLIP 3.69

https://launchpad.net/~plessy/+archive/plessy/+sourcepub/1547062/+listing-archive-extra
https://launchpad.net/~plessy/+archive/plessy/+sourcepub/1547739/+listing-archive-extra

(the second one is scheduled to be built in 2 hours, so I can not guarantee that it
will be available)

Can you try them ?

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


From wolfgang.rumpf at gmail.com  Mon Mar 14 17:49:57 2011
From: wolfgang.rumpf at gmail.com (Wolfgang Rumpf)
Date: Mon, 14 Mar 2011 13:49:57 -0400
Subject: [EMBOSS] HELP! fdnapars fails with undefined symbol error -
	ajSeqdbInit
In-Reply-To: <20110311155406.GQ2316@merveille.plessy.net>
References: <AANLkTi=26BHQz7dVR4yqJCu745sJ_u8=u56BPCzdfEGG@mail.gmail.com>
	<AANLkTinex6DHoa33L=wUv8iXuUNhdjfOMcoSuzDt=rd0@mail.gmail.com>
	<20110310013700.GC11010@merveille.plessy.net>
	<4D798864.9090801@gmail.com>
	<20110311155406.GQ2316@merveille.plessy.net>
Message-ID: <E6E1C183-5C21-43C5-92EE-F459C8705CCE@gmail.com>

Now when I run the application I get this error in fdnapars:

"Error:  Unable to read sequence '/var/lib/emboss-explorer/output/672342/.sequence'
Died:  fdnapars terminated:  Bad value for ' -sequence' with -auto defined"

I looked in that directory and all that was in there was a .sequence file that looked just fine (it was my input file)....any ideas what went wrong?  Running fdnapars from the command line also results in an error reading the sequence file (it's one I use for testing, worked fine previously)....


Wolfgang

Dr. Wolfgang Rumpf
Product Specialist, Rescentris Inc.
Adjunct Faculty, Dept. of Biotechnology, UMUC
--------------------------------------------------------
wolfgang.rumpf at rescentris.com
wolfgang.rumpf at gmail.com

Mobile - (614) 638-6797
Skype - wolfgang.rumpf



On Mar 11, 2011, at 10:54 AM, Charles Plessy wrote:

> Le Thu, Mar 10, 2011 at 09:26:44PM -0500, Wolfgang Rumpf a ?crit :
>> Also tried and failed - apparently there were dependencies that
>> couldn't be resolved.
> 
> I have prepared unofficial backports of EMBOSS 6.3.1 and EMBASSY-PHYLIP 3.69
> 
> https://launchpad.net/~plessy/+archive/plessy/+sourcepub/1547062/+listing-archive-extra
> https://launchpad.net/~plessy/+archive/plessy/+sourcepub/1547739/+listing-archive-extra
> 
> (the second one is scheduled to be built in 2 hours, so I can not guarantee that it
> will be available)
> 
> Can you try them ?
> 
> Have a nice day,
> 
> -- 
> Charles Plessy
> Debian Med packaging team,
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan




From marvin.stodolsky at gmail.com  Tue Mar 15 17:27:00 2011
From: marvin.stodolsky at gmail.com (Marvin Stodolsky)
Date: Tue, 15 Mar 2011 13:27:00 -0400
Subject: [EMBOSS] trimming mRNA to coding region, enroute to dicodon analysis
Message-ID: <AANLkTik9xu64sNwm1NYNddD4JCdPEj1LU2z6ZnV9fHB7@mail.gmail.com>

Starting with a large mRNA  fasta repository,
what is the route to generating a derivative with the untranslated
leader and post-stop codon segments trimmed off the mRNAs

This is enroute to a dicodon usage analysis, already written as a BASH
script calling PERL modules.
If anyone is interested in such applications, let me know.
pdc (parse dicodons) works fine, taking about a second per pre-trimmed
mRNA as it retreives from a FASTA repository.
But before providing it to a Novice community, some fool proofing best be done.

Marvin.Stodolsky at gmail.com


From wolfgang.rumpf at gmail.com  Tue Mar 15 20:49:47 2011
From: wolfgang.rumpf at gmail.com (Wolfgang Rumpf)
Date: Tue, 15 Mar 2011 16:49:47 -0400
Subject: [EMBOSS] Vienna in Emboss/Emboss-Explorer on Ubuntu?
Message-ID: <FA6E6854-923D-4EF4-B554-4C8F60461E54@gmail.com>

One of the ideas I try to teach in my bioinformatics class is RNA folding - and as such I'd love to add an RNA folding algorithm to my bioinformatics server.  It seems like the "easiest" path might be Vienna since there's an EMBOSS port of it.  I'm not sure how to proceed, however - I've downloaded the source (VIENNA-1.7.2) and know the rough procedure for getting it installed, but I want it to "hook in" to my existing Ubuntu EMBOSS-Explorer (which is how my students access all of the other analyses we do).  Any ideas how to modify the installation to install to the correct path so that it will be available in my existing applications list?

Any help appreciated - thanks in advance!


Wolfgang

Dr. Wolfgang Rumpf
Product Specialist, Rescentris Inc.
Adjunct Faculty, Dept. of Biotechnology, UMUC
--------------------------------------------------------
wolfgang.rumpf at rescentris.com
wolfgang.rumpf at gmail.com

Mobile - (614) 638-6797
Skype - wolfgang.rumpf






From david.bauer at bayer.com  Wed Mar 16 08:13:25 2011
From: david.bauer at bayer.com (david.bauer at bayer.com)
Date: Wed, 16 Mar 2011 09:13:25 +0100
Subject: [EMBOSS] Antwort:  trimming mRNA to coding region,
 enroute to dicodon analysis
In-Reply-To: <AANLkTik9xu64sNwm1NYNddD4JCdPEj1LU2z6ZnV9fHB7@mail.gmail.com>
Message-ID: <OF3F3EDBF1.495F0438-ONC1257855.002C6B49-C1257855.002D2CB8@bayer.de>

Hi,

I already sometimes thought it would be nice to have an option for getorf 
which would return just the longest ORF it finds. 
Here is what I use to get the coding part from an mRNA sequence if there 
is no feature table information:

> getorf test.fa -find 1 -norev | infoseq -only -len -desc -filter | sort 
-nr | head -1 | tr -d "[]" | awk '{print "seqret test.fa -sb "$2" -send 
"$4}'

HTH,
David.

emboss-bounces at lists.open-bio.org schrieb am 15/03/2011 18:27:00:

> Starting with a large mRNA  fasta repository,
> what is the route to generating a derivative with the untranslated
> leader and post-stop codon segments trimmed off the mRNAs
> 
> This is enroute to a dicodon usage analysis, already written as a BASH
> script calling PERL modules.
> If anyone is interested in such applications, let me know.
> pdc (parse dicodons) works fine, taking about a second per pre-trimmed
> mRNA as it retreives from a FASTA repository.
> But before providing it to a Novice community, some fool proofing 
> best be done.
> 
> Marvin.Stodolsky at gmail.com
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss


From david.bauer at bayer.com  Wed Mar 16 09:25:28 2011
From: david.bauer at bayer.com (david.bauer at bayer.com)
Date: Wed, 16 Mar 2011 10:25:28 +0100
Subject: [EMBOSS] Antwort:  Vienna in Emboss/Emboss-Explorer on Ubuntu?
In-Reply-To: <FA6E6854-923D-4EF4-B554-4C8F60461E54@gmail.com>
Message-ID: <OF827F9BEE.E42D2CBA-ONC1257855.00331892-C1257855.0033C616@bayer.de>

Hi,

the emboss-explorer creates the html menu on the fly by calling the emboss 
program wossname.
So if you install the Vienna embassy package just in the same place like 
the main emboss, the vrnafold etc. should appear in the emboss-explorer.
But I'm not using it on Ubuntu so I do not know if there are any Ubuntu 
specific issues.

HTH,
David.

emboss-bounces at lists.open-bio.org schrieb am 15/03/2011 21:49:47:

> One of the ideas I try to teach in my bioinformatics class is RNA 
> folding - and as such I'd love to add an RNA folding algorithm to my
> bioinformatics server.  It seems like the "easiest" path might be 
> Vienna since there's an EMBOSS port of it.  I'm not sure how to 
> proceed, however - I've downloaded the source (VIENNA-1.7.2) and 
> know the rough procedure for getting it installed, but I want it to 
> "hook in" to my existing Ubuntu EMBOSS-Explorer (which is how my 
> students access all of the other analyses we do).  Any ideas how to 
> modify the installation to install to the correct path so that it 
> will be available in my existing applications list?
> 
> Any help appreciated - thanks in advance!
> 
> 
> Wolfgang
> 
> Dr. Wolfgang Rumpf
> Product Specialist, Rescentris Inc.
> Adjunct Faculty, Dept. of Biotechnology, UMUC
> --------------------------------------------------------
> wolfgang.rumpf at rescentris.com
> wolfgang.rumpf at gmail.com
> 
> Mobile - (614) 638-6797
> Skype - wolfgang.rumpf
> 
> 
> 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss


From wolfgang.rumpf at gmail.com  Wed Mar 16 14:11:26 2011
From: wolfgang.rumpf at gmail.com (Wolfgang Rumpf)
Date: Wed, 16 Mar 2011 10:11:26 -0400
Subject: [EMBOSS] Antwort:  Vienna in Emboss/Emboss-Explorer on Ubuntu?
In-Reply-To: <OF827F9BEE.E42D2CBA-ONC1257855.00331892-C1257855.0033C616@bayer.de>
References: <OF827F9BEE.E42D2CBA-ONC1257855.00331892-C1257855.0033C616@bayer.de>
Message-ID: <17E9EBB9-92C3-44E7-8CB8-381A32386982@gmail.com>

David, I suspected as much - I think my real concern is that I don't necessarily know the proper command-line syntax to control where the installation occurs.  My EMBOSS proper is in /usr/lib/emboss/; there appear to be additional files in /usr/share/emboss (e.g. acd, data, doc) and in /usr/share/emboss-explorer.  These should be the default locations for the packages from the Software Center in Ubuntu.

So given that, when I configure Vienna, do I tell Vienna that it will live in /usr/share/emboss by typing  ./configure --prefix=/usr/lib/emboss - or is there something I'm missing?


Wolfgang

Dr. Wolfgang Rumpf
Product Specialist, Rescentris Inc.
Adjunct Faculty, Dept. of Biotechnology, UMUC
--------------------------------------------------------
wolfgang.rumpf at rescentris.com
wolfgang.rumpf at gmail.com

Mobile - (614) 638-6797
Skype - wolfgang.rumpf



On Mar 16, 2011, at 5:25 AM, david.bauer at bayer.com wrote:

> 
> Hi, 
> 
> the emboss-explorer creates the html menu on the fly by calling the emboss program wossname. 
> So if you install the Vienna embassy package just in the same place like the main emboss, the vrnafold etc. should appear in the emboss-explorer. 
> But I'm not using it on Ubuntu so I do not know if there are any Ubuntu specific issues. 
> 
> HTH, 
> David. 
> 
> emboss-bounces at lists.open-bio.org schrieb am 15/03/2011 21:49:47:
> 
> > One of the ideas I try to teach in my bioinformatics class is RNA 
> > folding - and as such I'd love to add an RNA folding algorithm to my
> > bioinformatics server.  It seems like the "easiest" path might be 
> > Vienna since there's an EMBOSS port of it.  I'm not sure how to 
> > proceed, however - I've downloaded the source (VIENNA-1.7.2) and 
> > know the rough procedure for getting it installed, but I want it to 
> > "hook in" to my existing Ubuntu EMBOSS-Explorer (which is how my 
> > students access all of the other analyses we do).  Any ideas how to 
> > modify the installation to install to the correct path so that it 
> > will be available in my existing applications list?
> > 
> > Any help appreciated - thanks in advance!
> > 
> > 
> > Wolfgang
> > 
> > Dr. Wolfgang Rumpf
> > Product Specialist, Rescentris Inc.
> > Adjunct Faculty, Dept. of Biotechnology, UMUC
> > --------------------------------------------------------
> > wolfgang.rumpf at rescentris.com
> > wolfgang.rumpf at gmail.com
> > 
> > Mobile - (614) 638-6797
> > Skype - wolfgang.rumpf
> > 
> > 
> > 
> > 
> > _______________________________________________
> > EMBOSS mailing list
> > EMBOSS at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/emboss




From wolfgang.rumpf at gmail.com  Wed Mar 16 14:54:16 2011
From: wolfgang.rumpf at gmail.com (Wolfgang Rumpf)
Date: Wed, 16 Mar 2011 10:54:16 -0400
Subject: [EMBOSS] Antwort: Vienna in Emboss/Emboss-Explorer on Ubuntu?
In-Reply-To: <E6C88150E7007C4F8BA51F1F5DD4C0E9042FA3A341@UMMSCSMAIL01.ad.umassmed.edu>
References: <OF827F9BEE.E42D2CBA-ONC1257855.00331892-C1257855.0033C616@bayer.de>
	<17E9EBB9-92C3-44E7-8CB8-381A32386982@gmail.com>
	<E6C88150E7007C4F8BA51F1F5DD4C0E9042FA3A341@UMMSCSMAIL01.ad.umassmed.edu>
Message-ID: <899D5FD0-5211-40F7-9592-C65E108D887A@gmail.com>

I most certainly am HOPING to use the embassy package - that's the one I downloaded.  Again, is there any special command I need to use during the ./configure process in order to ensure that it goes into the correct locations (those corresponding to the locations where Emboss/Embassy were installed by the precompiled binaries from the Ubuntu Software Center)?  To clarify - I did NOT compile emboss/embassy myself; the Ubuntu Software Center installed those for me.  But now I want to add Vienna, and must do so by compiling, and I want it to "seamlessly" work with my existing Emboss/Embassy install....


Wolfgang

Dr. Wolfgang Rumpf
Product Specialist, Rescentris Inc.
Adjunct Faculty, Dept. of Biotechnology, UMUC
--------------------------------------------------------
wolfgang.rumpf at rescentris.com
wolfgang.rumpf at gmail.com

Mobile - (614) 638-6797
Skype - wolfgang.rumpf



On Mar 16, 2011, at 10:50 AM, Lapointe, David wrote:

> Are you using the embassy package for ViennaRNA? That compiles along with EMBOSS and ends up quite nicely with emboss-explorer. Use the software from here ftp://emboss.open-bio.org/pub/EMBOSS/  so the acd files are created.
> 
> David
> 
> --
> David Lapointe, Ph.D.
> Director Scientific Computing/Information Services
> University of Massachusetts Medical School
> 55 Lake Avenue N
> Worcester MA 01655
> 508-856-5141 (v)
> 
> 
> 
> -----Original Message-----
> From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Wolfgang Rumpf
> Sent: Wednesday, March 16, 2011 10:11 AM
> To: david.bauer at bayer.com
> Cc: emboss at lists.open-bio.org
> Subject: Re: [EMBOSS] Antwort: Vienna in Emboss/Emboss-Explorer on Ubuntu?
> 
> David, I suspected as much - I think my real concern is that I don't necessarily know the proper command-line syntax to control where the installation occurs.  My EMBOSS proper is in /usr/lib/emboss/; there appear to be additional files in /usr/share/emboss (e.g. acd, data, doc) and in /usr/share/emboss-explorer.  These should be the default locations for the packages from the Software Center in Ubuntu.
> 
> So given that, when I configure Vienna, do I tell Vienna that it will live in /usr/share/emboss by typing  ./configure --prefix=/usr/lib/emboss - or is there something I'm missing?
> 
> 
> Wolfgang
> 
> Dr. Wolfgang Rumpf
> Product Specialist, Rescentris Inc.
> Adjunct Faculty, Dept. of Biotechnology, UMUC
> --------------------------------------------------------
> wolfgang.rumpf at rescentris.com
> wolfgang.rumpf at gmail.com
> 
> Mobile - (614) 638-6797
> Skype - wolfgang.rumpf
> 
> 
> 
> On Mar 16, 2011, at 5:25 AM, david.bauer at bayer.com wrote:
> 
>> 
>> Hi, 
>> 
>> the emboss-explorer creates the html menu on the fly by calling the emboss program wossname. 
>> So if you install the Vienna embassy package just in the same place like the main emboss, the vrnafold etc. should appear in the emboss-explorer. 
>> But I'm not using it on Ubuntu so I do not know if there are any Ubuntu specific issues. 
>> 
>> HTH, 
>> David. 
>> 
>> emboss-bounces at lists.open-bio.org schrieb am 15/03/2011 21:49:47:
>> 
>>> One of the ideas I try to teach in my bioinformatics class is RNA 
>>> folding - and as such I'd love to add an RNA folding algorithm to my
>>> bioinformatics server.  It seems like the "easiest" path might be 
>>> Vienna since there's an EMBOSS port of it.  I'm not sure how to 
>>> proceed, however - I've downloaded the source (VIENNA-1.7.2) and 
>>> know the rough procedure for getting it installed, but I want it to 
>>> "hook in" to my existing Ubuntu EMBOSS-Explorer (which is how my 
>>> students access all of the other analyses we do).  Any ideas how to 
>>> modify the installation to install to the correct path so that it 
>>> will be available in my existing applications list?
>>> 
>>> Any help appreciated - thanks in advance!
>>> 
>>> 
>>> Wolfgang
>>> 
>>> Dr. Wolfgang Rumpf
>>> Product Specialist, Rescentris Inc.
>>> Adjunct Faculty, Dept. of Biotechnology, UMUC
>>> --------------------------------------------------------
>>> wolfgang.rumpf at rescentris.com
>>> wolfgang.rumpf at gmail.com
>>> 
>>> Mobile - (614) 638-6797
>>> Skype - wolfgang.rumpf
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
> 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
> 
> 




From david.bauer at bayer.com  Wed Mar 16 15:36:36 2011
From: david.bauer at bayer.com (david.bauer at bayer.com)
Date: Wed, 16 Mar 2011 16:36:36 +0100
Subject: [EMBOSS] Antwort: Re: Antwort: Vienna in Emboss/Emboss-Explorer on
	Ubuntu?
In-Reply-To: <899D5FD0-5211-40F7-9592-C65E108D887A@gmail.com>
Message-ID: <OF17552755.555B72AA-ONC1257855.0054F785-C1257855.0055C064@bayer.de>

Hi Wolfgang, 

mixing precompiled package installation with installations from source is 
dangerous and something one should never ever do.
In the normal emboss installation procedure (from source) you put the 
embassy packages within the source tree of emboss and run the compilation 
and installation from this place.
When I look at the directories you mention, where the emboss package is 
installed, this seems to be very ubuntu specific. So I hope someone who is 
familiar with ubuntu and/or the emboss package can help you with this.

David.

emboss-bounces at lists.open-bio.org schrieb am 16/03/2011 15:54:16:

> I most certainly am HOPING to use the embassy package - that's the 
> one I downloaded.  Again, is there any special command I need to use
> during the ./configure process in order to ensure that it goes into 
> the correct locations (those corresponding to the locations where 
> Emboss/Embassy were installed by the precompiled binaries from the 
> Ubuntu Software Center)?  To clarify - I did NOT compile 
> emboss/embassy myself; the Ubuntu Software Center installed those 
> for me.  But now I want to add Vienna, and must do so by compiling, 
> and I want it to "seamlessly" work with my existing Emboss/Embassy 
install....
> 
> 
> Wolfgang
> 
> Dr. Wolfgang Rumpf
> Product Specialist, Rescentris Inc.
> Adjunct Faculty, Dept. of Biotechnology, UMUC
> --------------------------------------------------------
> wolfgang.rumpf at rescentris.com
> wolfgang.rumpf at gmail.com
> 
> Mobile - (614) 638-6797
> Skype - wolfgang.rumpf
> 
> 
> 
> On Mar 16, 2011, at 10:50 AM, Lapointe, David wrote:
> 
> > Are you using the embassy package for ViennaRNA? That compiles 
> along with EMBOSS and ends up quite nicely with emboss-explorer. Use
> the software from here ftp://emboss.open-bio.org/pub/EMBOSS/  so the
> acd files are created.
> > 
> > David
> > 
> > --
> > David Lapointe, Ph.D.
> > Director Scientific Computing/Information Services
> > University of Massachusetts Medical School
> > 55 Lake Avenue N
> > Worcester MA 01655
> > 508-856-5141 (v)
> > 
> > 
> > 
> > -----Original Message-----
> > From: emboss-bounces at lists.open-bio.org [mailto:emboss-
> bounces at lists.open-bio.org] On Behalf Of Wolfgang Rumpf
> > Sent: Wednesday, March 16, 2011 10:11 AM
> > To: david.bauer at bayer.com
> > Cc: emboss at lists.open-bio.org
> > Subject: Re: [EMBOSS] Antwort: Vienna in Emboss/Emboss-Explorer on 
Ubuntu?
> > 
> > David, I suspected as much - I think my real concern is that I 
> don't necessarily know the proper command-line syntax to control 
> where the installation occurs.  My EMBOSS proper is in 
> /usr/lib/emboss/; there appear to be additional files in 
> /usr/share/emboss (e.g. acd, data, doc) and in /usr/share/emboss-
> explorer.  These should be the default locations for the packages 
> from the Software Center in Ubuntu.
> > 
> > So given that, when I configure Vienna, do I tell Vienna that it 
> will live in /usr/share/emboss by typing  ./configure --
> prefix=/usr/lib/emboss - or is there something I'm missing?
> > 
> > 
> > Wolfgang
> > 
> > Dr. Wolfgang Rumpf
> > Product Specialist, Rescentris Inc.
> > Adjunct Faculty, Dept. of Biotechnology, UMUC
> > --------------------------------------------------------
> > wolfgang.rumpf at rescentris.com
> > wolfgang.rumpf at gmail.com
> > 
> > Mobile - (614) 638-6797
> > Skype - wolfgang.rumpf
> > 
> > 
> > 
> > On Mar 16, 2011, at 5:25 AM, david.bauer at bayer.com wrote:
> > 
> >> 
> >> Hi, 
> >> 
> >> the emboss-explorer creates the html menu on the fly by calling 
> the emboss program wossname. 
> >> So if you install the Vienna embassy package just in the same 
> place like the main emboss, the vrnafold etc. should appear in the 
> emboss-explorer. 
> >> But I'm not using it on Ubuntu so I do not know if there are any 
> Ubuntu specific issues. 
> >> 
> >> HTH, 
> >> David. 
> >> 
> >> emboss-bounces at lists.open-bio.org schrieb am 15/03/2011 21:49:47:
> >> 
> >>> One of the ideas I try to teach in my bioinformatics class is RNA 
> >>> folding - and as such I'd love to add an RNA folding algorithm to my
> >>> bioinformatics server.  It seems like the "easiest" path might be 
> >>> Vienna since there's an EMBOSS port of it.  I'm not sure how to 
> >>> proceed, however - I've downloaded the source (VIENNA-1.7.2) and 
> >>> know the rough procedure for getting it installed, but I want it to 
> >>> "hook in" to my existing Ubuntu EMBOSS-Explorer (which is how my 
> >>> students access all of the other analyses we do).  Any ideas how to 
> >>> modify the installation to install to the correct path so that it 
> >>> will be available in my existing applications list?
> >>> 
> >>> Any help appreciated - thanks in advance!
> >>> 
> >>> 
> >>> Wolfgang
> >>> 
> >>> Dr. Wolfgang Rumpf
> >>> Product Specialist, Rescentris Inc.
> >>> Adjunct Faculty, Dept. of Biotechnology, UMUC
> >>> --------------------------------------------------------
> >>> wolfgang.rumpf at rescentris.com
> >>> wolfgang.rumpf at gmail.com
> >>> 
> >>> Mobile - (614) 638-6797
> >>> Skype - wolfgang.rumpf
> >>> 
> >>> 
> >>> 
> >>> 
> >>> _______________________________________________
> >>> EMBOSS mailing list
> >>> EMBOSS at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/emboss
> > 
> > 
> > _______________________________________________
> > EMBOSS mailing list
> > EMBOSS at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/emboss
> > 
> > 
> 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss


From stefanielager at gmail.com  Wed Mar 23 10:00:35 2011
From: stefanielager at gmail.com (Stefanie Lager)
Date: Wed, 23 Mar 2011 12:00:35 +0200
Subject: [EMBOSS] How to include homing endonucleases?
Message-ID: <AANLkTimVLvUKG1Y7ncZiCAQ-G5dv0ZavheBjqKBj5xiA@mail.gmail.com>

Hi,

Rebase got a separate file listing all homing  endonuclease
(ftp://ftp.neb.com/pub/rebase/homing.103), how can I index that file
as an alternative to rebase? The Emboss  program restrict have the
option to use a specific datafile, but it's not clear what format that
file should be?

Regards,

Stefanie Lager


From witch.of.agnessi at gmail.com  Wed Mar 23 20:46:01 2011
From: witch.of.agnessi at gmail.com (B Enn)
Date: Wed, 23 Mar 2011 16:46:01 -0400
Subject: [EMBOSS] the -orfminsize in SIXPACK and -minsize in GETORF
Message-ID: <AANLkTin5WfRdcC36QoLCi3namBzucV2b05fphAwD_FjR@mail.gmail.com>

Are the options -orfminsize in SIXPACK and -minsize in GETORF the same?

Do they both specify "Minimum nucleotide size of ORF to report"?

Are these two programs supposed to give the same results under identical
input parameters?

Thanks


From smehr at amnh.org  Thu Mar 31 21:14:33 2011
From: smehr at amnh.org (Shaadi Pooyaei Mehr)
Date: Thu, 31 Mar 2011 17:14:33 -0400
Subject: [EMBOSS] getorf executable
Message-ID: <019BC523-C8BB-422F-AE87-5AD4D728F55C@amnh.org>

Hi all, 

I have downloaded the EMBOSS 6.3.1 but the "getorf" executable is not part of it ! Do I need to get the separate CVS file? If so which one do I need to get?


Best